• 한국동물위생학회지
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• 제32권1호
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• pp.1-10
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• 2009

In order to obtain the genetic information of the Korean isolates of porcine circovirus 2 (PCV2), complete genomes of five isolates from Korean PCVD weaned pigs with wasting syndromes were sequenced and compared with those of other published PCV2 isolates. Of the five PCV2 isolates, four (1767 nucleotides) were classified into PCV2b, and one (1,768 nucleotides) was PCV2a. Moreover, it appeared that PCV2b is now the dominant genotype circulating in Korea herds. Total complete genomes of four PCV2b isolates shared $99.1{\sim}99.4%$ nucleotide sequence homology each other, and were only $95.4{\sim}96.2%$ similar to one PCV2a isolate. ORF2 genome of four PCV2b isolates shared over 99% nucleotide sequence and deduced amino acid sequence identity to each other. Nevertheless, those were much divergent with the PCV2a isolate of this study and ranged from $92.3{\sim}92.7%$ nucleotide homology and $91.9{\sim}92.3%$ deduced amino acid sequence homology, respectively. The amino acid sequence alignments of the putative capsid protein identified three major regions of amino acid heterogeneity at residues $59{\sim}91$, $121{\sim}136$ and $190{\sim}210$. Two of those correspond with dominant immunoreactive areas. Phylogenetic analysis based on the complete genome of PCV2 isolates showed that four PCV2b isolates of this study existed the closest relationship with European strains (Netherland, UK and France). One PCV2a isolate was closely related to Japan and North America strains.

• 대한수의학회지
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• 제42권1호
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• pp.89-100
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• 2002

The nonstructural glycoprotein NSP4, encoded by the 10th gene of rotavirus, has been known to play important roles in viral assembly and pathogenesis. The NSP4 genes of human rotavirus Korean isolates, designated as CBNU/HR-1, CBNU/HR-2, CBNU/HR-3, and CBNU/HR-4, were cloned, sequenced and characterized. Also, the NSP4 gene of the CBNU/HR-1 was expressed in a baculovirus-insect cell system. The sequence data indicated that the NSP4 genes of human rotavirus Korean isolates were 750 or 751 bases in length and encoded one open reading frame of 175 amino acids. Two glycosylation sites were recognized in the NSP4 gene of human rotavirus isolates tested. The NSP4 of CBNU/HR-1, CBNU/HR-3, and CBNU/HR-4 exhibited a high degree of amino acid sequence homology with that of NSP4 genotype B viruses, but a low degree of amino acid sequence homology with that of NSP4 genotype A viruses. However, the NSP4 of CBNU/HR-2 exhibited a high degree of amino acid sequence homology with that of NSP4 genotype A viruses, but a low degree of amino acid sequence homology with that of NSP4 genotype B viruses. The Sf9 cells infected with recombinant baculovirus, inserted with NSP4 gene of CBNU/HR-1, produced specific cytopathic effects and the expressed NSP4 was detected by immunofluorescence staining using NSP4-specific monoclonal antibody(MAb). The expressed NSP4 migrated at 16-26 kDa on SDS-PAGE and reacted with NSP4-specific MAb by Western blotting.

• Journal of Life Science
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• 제9권1호
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• pp.84-89
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• 1999

To determine phylogenetic relatedness of four silk-producing silkmoths (B. mori, B. mandarina, A. yamamai and A. pernyi), internal coding region of arylphorin which is a storage protein in hemolymph protein of insects were amplified by polymerase chain reaction and then sequenced and compared each other. The nucleotide composition was biased toward adenine and thymine(59% A+T) and a strong bias for use of C in the third position of codons was found for Phe and Tyr. Together TTC(Phe) and TAC(Tyr) account for about 16.8% (10 for TTC and 8 for TAC) of all codon usage. The nucleotide similarity of arylphorin gene from B. mori showed 99%, 98% and 97% homology with those of B. mandarina, A. yamamai and A. pernyi, respectively. Also, the nucleotide sequence of arylphorin gene from B. mandarina showed 98% and 97% homology with those of A. yamamai and A.pernyi, respectively. Between A. yamamai and A. pernyi, the sequence homology was 97%. The deduced amino acid sequences in B. mori, B. mandarina and A. yamamai showed almost 99% homology. Although the aryphorin gene provided insufficient variability among the four insect species, A UPGMA tree is generated that supported the monophyly of silk-producing insects, with M. sexta placed basal to it. It is suggest that silk-producing insects have a close relationship and a homogeneous genetic background from comparison with those of other insects.

• 한국컴퓨터그래픽스학회논문지
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• 제2권2호
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• pp.61-68
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• 1996

본 논문에서는 대용량의 DNA 염기 배열의 정성 정보를 특징짓기 위한 새로운 가시화 방법을 제안한다. DNA 배열은 배열 자체가 방대한 양의 정보를 포함하고 있기 때문에 분석에 많은 어려움이 있다. 우리는 DNA 염기 배열들사이의 상사성 비교를 위해 DNA 염기 배열을 하나의 이미지 도메인으로 변환한다. 프로그램은 random walk plot으로 DNA 염기 배열을 가시화한 후에 k-convex hull로 단순화 시킨다. Random Walk plot은 염기배열을 평면상에 하나의 커브로 표현한다. k-convex hull은 walk plot으로부터 무의미한 부분을 제거함으로서 walk plot을 단순화한다. 이러한 방법은 유전공학자들에게 쉽게 DNA 배열의 특징을 인식하고 분류할 수 있는 직관을 제공한다. 실제 게놈 데이터로 실험한 결과는 논문에서 제안하는 방법이 긴 DNA 염기배열들 사이의 유사성 분석을 위해 좋은 가시화 도구임을 보여준다.

• 미생물학회지
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• 제30권5호
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• pp.397-402
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• 1992

서울지역의 소아설사환자가 가검물로부터 분리한 로타바이러스의 VP7을 코딩하는 RNA분절 cDNA를 합성한 후 로타바이러스 혈청형1인 WA1과 RE9의 아홉 번째 RNA분절과 비교하였더니 90%이상의 유사성을 보였다. 염기서열로부터 유추된 아미노산 서열중 혈청간에 변이가 많은 VR5와 VR8 지역을 비교한 결과 역시 혈청형 1인 RE9과 WA1 바이러스주와 매우 높은 유사성을 지님을 알 수 있었다.

• 통합자연과학논문집
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• 제8권1호
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• pp.13-18
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• 2015

Cysteinyl leukotrienes are inflammatory mediators having important role in pathophysiological conditions such as asthma, allergic rhinitis and have been implicated in a number of inflammatory conditions including cardiovascular and gastrointestinal diseases. Most of the disease regulatory actions of the CysLTs are mediated through CysLT1 receptor. Hence in the present study, homology modeling of CysLT1 was performed because the availability of 3D structure would enhance the development of new drugs for inflammatory diseases. However the templates identified have low sequence identity which increases the complexity of modeling. Hence, homology modeling was performed using single template, multiple templates and also using threading I-TASSER server. The best model was selected based on the validation of the generated models using Ramachandran and ERRAT plot. The model developed could be useful for identifying crucial residues and docking study.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.125.3-126
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• 2003

A near full-length sequence of a new tobamovirus infecting Hibiscus rosa-sinensis L. was determined. The genome consists of 58 nucleotides (nt) 5' UTR, followed by a 4.9 kb ORF which methyl transferase helicase domain (128 kDa), readthrough protein RNA dependent RNA polymerase (RdRp) 185 kDa and a 52 kDa protein. The 128 kDa protein had a maximum homology of 51.4 ％ to TMGMV and amino acids (an) were 54.3 ％ identical to TMV- vulgare strain. The 185 kDa RdRp had a maximum homology of 53.5％ to TMV-Ob and KGMMV-Y and a 59.6％ homology at the an level to CGMMV-SH. The MP gene encodes 282 aa and its theoretical molecular weight is 30.4 kDa. The nt and an sequence identities of MP ranged from 38.8％ to 43.9％ and 30.9％ to 37.9％, respectively. The CP gene encodes 163 residues and with a theoretical molecular weight of 18.2 kDa The (nt) and aa sequences of the CP were 46.9 ％ to 51.6％ and 45.3％ to 57.1％ identical to other tobamoviruses, respectively. The predicted virion origin of assembly (OAS) was located in the CP gene. Phylogenetic trees generated based on the nt and as sequences of RdRp, MP and CP genes indicated that this new virus clustered with subgroup II tobamoviruses. Although the CP ORF of this virus shared a high nt and aa sequence identity with Sunn-hemp mosaic virus (SHMV), Western analysis showed that it is serologically unrelated to SHMV. We propose the name Hibiscus virus S (HVS) for this Singapore isolate. This is the first report on a near full-length sequence of a Tobamovirus that infects hibiscus.

• The Plant Pathology Journal
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• 제18권2호
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• pp.98-101
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• 2002

Using phytoplasma universal primer pair Pl and P7, a fragment of about 1.8 kb nucleotide sequences of 16S rRNA gene and 16S-23S rRNA intergenic spacer region, and a portion of 23S rRNA gene of jujube witches'broom (JWB) and mulberry dwarf(MD) phytoplasmas were determined. The nucleotide sequences of JWB and MD were 1,850 bp and 1,831 bp long, respectively. The JWB phytoplasma sequence was aligned with the homologous sequence of MD phytoplasma. Twenty-eight base insertions and nine base deletions were found in the JWB phytoplasma sequence compared with that of MD phytoplasma. The similarity of the aligned sequences of JWB and MD was 84.8%. The near-complete 16S rRNA gene DNA sequences of JWB and MD were 1,529 bp and 1,530 bp in length, respectively, and revealed 89.0% homology. The 16S-23S rRNA intergenic spacer region DNA sequences were 263 bp and 243 bp in lengths respectively, while homology was only 70% and the conserved tRNA-lle gene of JWB and MD was located into the intergenic space region between 16S-23S rRNA gene. The nucleotide sequences were 77 bp long in both JWB and MD, and showed 97.4% sequence homology. Based on the phylogenetic analysis of the two phytoplasmas, the JWB phytoplasma belongs to the Elm yellow phytoplasma group (16S rV), whereas, the MD phytoplasma belongs to the Aster yellow group (16S rI).

• 한국수산과학회지
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• 제45권3호
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• pp.238-245
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• 2012

In this study, the molecular structures of tet(M) and tet(G) carried by tetracycline (Tc) resistant bacteria in intestinal microflora from the imported ornamental fish were characterized and compared with each other depend on the imported countries. Of the total isolates, approximately 8.9% of the Ent-lac+(lactose fermentative bacteria on coliform media) Tc resistant isolates in fish from three different countries, Singapore, Taiwan and Brazil, were appeared to contain tet(M). Three representative isolates of different countries, Aeromonas spp. JSM-1 (Singapore), JTM-1 (Taiwan) and JBM-1 (Brazil), were isolated and analyzed the molecular structures of tet(M) gene. Interestingly, partial sequence of tet(M) genes (1099 bp) in JBM-1 (Brazil) showed 99.5% homology with the tet(M) found in the Vibrio spp. RV16 isolate, obtained from marine fish in Korea and known to carry Tn1545 parent type of tet(M). In contrast, tet(M) gene in JSM-1 and JTM-1 showed mosaic structure of Tn1545 and Tn916, and 100% homology with each other. It may suggest the presence of various characteristics in terms of tet(M) gene structure. The determined sequence of the tet(G) from Aeromonas spp. JSG-1 and JBG-1 isolated from Singapore and Indonesia ornamental fish respectively showed similar nucleotide sequence homology but revealed a few nucleotide changes in comparison with the sequence of the prototype tet(G) gene (S52437 in GenBank).

• Journal of Microbiology and Biotechnology
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• 제13권3호
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• pp.457-462
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• 2003

The complete nucleotide sequence of a plasmid, pMG1, isolated from Bifidobacterium longum MG1 has been determined. This plasmid, composed of 3,862 base pairs with 65.1% of G+C content. harbors two major open reading frames (ORF) encoding putative proteins of 29 kDa (ORF I) and 71 kDa (ORF II). ORF I showed relatively high amino acid sequence homology with replication proteins of other plasmids from Gr Im-positive and -negative bacteria. Upstream of ORF I, four sets of tandem repeat sequences resembling the iteron structure of related plasmids were found. S1 endonuclease treatment and Southern blot analysis revealed that pMG1 accumulates single-stranded DNA (ssDNA) intermediate, which indicate i the rolling circle replication (RCR) mechanism of this plasmid. Homology search indicated that ORF II encodes plasmid mobilization protein, and the presence of highly conserved oriT sequence in the upstream of this gene supported this assumption. RT-PCR showed that only ORF I is expressed in vivo. Based on these results, pMG 1 was exploited to construct a shuttle vector, pBES2. It was successfully transformed into Bifidobacterium and maintained stably.