• Journal of the korean society of oceanography
• /
• 제39권3호
• /
• pp.163-171
• /
• 2004

Sequences of the large subunit ribosomal (LSD) rDNA D1-D2 region of Alexandrium catenella(=A. sp. cf. catenella) and A. tamarense isolates, which were collected along the Korea coasts, were analyzed to understand their phylogenetic relationships and geographical distributions. All A. catenella and A. tamarense isolates belonged to the A. tamarense/catenella/fundyense complex and were grouped with the North American and temperate Asian ribotypes, respectively, regardless of the presence or absence of a ventral pore in the first apical plate. A consistent and peculiar characteristic that differentiated the Alexandrium isolates was amplification of a second PCR product with a lower molecular weight in addition to the predicted one; ten A. catenella isolates belonging to the temperate Asian ribotype yielded this additional PCR product. Sequence alignment revealed that the shorter PCR product resulted from an unusual large deletion of 87 bp in the LSD rDNA D1 domain. The North American and temperate Asian ribotypes were prevalent along the Korean coasts without geographical separation. Given the high genetic homogeneity among widely distributed Alexandrium populations, each ribotype appeared to be pandemic rather than to constitute a distinct regional population.

• The Plant Pathology Journal
• /
• 제25권1호
• /
• pp.47-53
• /
• 2009

Sequence analysis of the Chlorella virus SS-2 revealed one putative nuclease gene that is 807 bp long and encodes a 31kDa protein. Multiple sequence alignment analysis reveals the presence of highly conserved PD-(D/E)XK residues in the encoded protein. The gene cloned into an expression vector was expressed as a His-tagged fusion protein in chaperone containing pKJE7 cells. The recombinant protein was purified using a His-Trap chelating HP column and used for functional analysis. Exonuclease activity of the SS-2 nuclease was detected when the DNA substrates, such as linear ssDNA, PCR amplicon, linear dsDNA with 5'-overhang ends, 3'-overhang ends, or blunt ends were used. Covalently closed circular DNA was also degraded by the SS-2 recombinant protein, suggesting that the SS-2 nuclease has an endonuclease activity. Stable activity of SS-2 nuclease was observed between $10^{\circ}C$ and $50^{\circ}C$. The optimum pH concentrations for the SS-2 nuclease were pH 6.0-8.5. Divalent ions inhibited the SS-2 nuclease activity.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제15권2호
• /
• pp.123-130
• /
• 2007

The Hsp 20.8 and Hsp 90 cDNA sequence retrieved from NCBI database and consists of 764 bp and 2582 bp lengths respectively. The corresponding cDNA homologus sequences were BLAST searched in Bombyx mori genomic DNA database and two genomic contigs viz., BAAB01120347 and AADK01011786 showed maximum homology. In B. mori Hsp 20.8 and Hsp 90 is encoded by single gene without intron. Specific primers were used to amplify the Hsp 20.8 gene and Hsp 90 variable region from genomic DNA by using the PCR. Obtained products were 216 bp in Hsp 20.8 and 437 bp in Hsp 90. There was no variation found in the six silkworm races PCR products size of contrasting response to thermal tolerance. The comparison of the sequenced nucleotide variations through multiple sequence alignment analysis of Hsp 90 variable region products of three races not showed any differences respect to their thermotolerance and formed the clusters among the voltinism. The comparison of aminoacid sequences of B. mori Hsps with dipteran and other insect taxa revealed high percentage of identity growing with phylogenetic relatedness of species. The conserved domains of B. mori Hsps predicted, in which the Hsp 20.8 possesses ${\alpha}-crystallin$ domain and Hsp 90 holds HATPase and Hsp 90 domains.

• 미생물학회지
• /
• 제35권2호
• /
• pp.121-127
• /
• 1999

염기서열 해독작업에서 각 핵산 단편을 조립하는 contig 구성문제에 활용이 가능한 computer program을 개발하였다. 본 프로그램은 국내에서 광범위하게 사용되고 있는 MS-Windows 운영체제의 개인용 컴퓨터에서 작동이 가능하며, GenBank, FASTA, ASCII 등과 같은 다양한 형태의 염기서열 자료를 입력할 수 있다. 두 단편에서 최대 유사도를 나타내는 부분을 정렬하는 작업에는 염기서열의 국부적 상동성을 계산하고 dynamic programming 알고리즘을 적용하는 방법을 이용하였다. 또한 사용하기 편리한 그래픽 방식의 인터페이스를 제공하여 초보자라도 손쉽게 조작할 수 있다는 장점을 갖는다. 본 프로그램의 성능을 검증하기 위하여 세균과 곰팡이로부터 해독된 16S rRNA 와 18S rRNA 유전자의 단편 염기서열을 재구성하는 작업에 프로그램을 사용하였을 때에 효율적인 작업이 가능하였다.

• 대한미생물학회지
• /
• 제34권6호
• /
• pp.561-571
• /
• 1999

Diagnosis of mycobacterial infection is dependent upon the isolation and identification of causative agents. The procedures involved are time consuming and technically demanding. To improve the laborious identification process mycobacterial systematics supported by gene analysis is feasible, being particularly useful for slowly growing or uncultivable mycobacteria. To complement genetic analysis for the differentiation and identification of mycobacterial species, an alternative marker gene, rpoB encoding the ${\beta}$ subunit of RNA polymerase, was investigated. rpoB DNAs (342 bp) were amplified from 52 reference strains of mycobacteria including Mycobacterium tuberculosis H37Rv (ATCC 27294) and clinical isolates by the PCR. The nucleotide sequences were directly determined (306 bp) and aligned using the multiple alignment algorithm in the MegAlign package (DNASTAR) and MEGA program. A phylogenetic tree was constructed with a neighborhood joining method. Comparative sequence analysis of rpoB DNA provided the basis for species differentiation. By being grouped into species-specific clusters with low sequence divergence among strains belonging to same species, all the clinical isolates could be easily identified. Furthermore RFLP analysis enabled rapid identification of clinical isolates.

• Journal of Microbiology
• /
• 제33권2호
• /
• pp.136-141
• /
• 1995

From a cluster of structural rRNA genes which has previsouly been cloned (Hwang and Kim, in submission; J. Microbiol. Biotechnol.), a 1.0-kb Eco RI fragment of DNA which shows significant homology to the 25S and rRNA s of Tricholoma matsutake was used for sequence analysis. Nucleotide sequence was bidirectionally determined using delection series of the DNA fragment. Comparing the resultant 1016-base sequence with sequences in the database, both the 3'end of 25S-rRNA gene and 5S rRNA gene were searched. The 5S rRNA gene is 118-bp in length and is located 158-bp downstream of 3'end of the 25S rRNA gene. IGSI and IGS2 (partial) sequences are also contained in the fragment. Multiple alignment of the 5S rRNA sequences was carried out with 5S rRNA sequences from some members of the subdivision Basidiomycotina obtained from the database. Polygenetic analysis with distance matrix established by Kimura's 2-parameter method and phylogenetic tree by UPGMA method proposed that T. matsutake is closely related to efibulobasidium allbescens. Secondary structure of 5S rRNA was also hypothesized to show similar topology with its generally accepted eukaryotic counterpart.

• 한국콘텐츠학회논문지
• /
• 제10권7호
• /
• pp.81-87
• /
• 2010

본 논문에서는 현재 생물정보학 연구에서 가장 많이 사용하고 있는 BLAST의 문제점을 분석하고 이에 따른 해결책을 제시하기 위하여 그리드 컴퓨팅을 이용한 G-BLAST(Grid Computing을 이용한 Basic Local Alignment Search Tool)를 제안한다. 본 연구에서 제안하고 있는 G-BLAST을 이용한 시스템은 이기종 분산 환경에서 수행이 가능한 서열분석 통합 소프트웨어 패키지이며 기존 서열분석 서비스의 취약점인 검색 성능을 개선하여 BLAST 검색 기능을 강화 하였다. 또한, BLAST 결과를 사용자가 관리 및 분석이 용이하도록 데이터베이스 및 유전체 서열분석 서비스 시스템을 구현하였다. 본 논문에서는 G-BLAST시스템의 성능확인을 위하여 병렬컴퓨팅 성능테스트 기법을 도입하여 구현된 시스템을 기존 BLAST와 속도 및 효율부분에서 비교하여 성능개선을 확인하였으며 서열결과 분석에 필요한 자료를 사용자관점에서 제공해주고 있다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제17권7호
• /
• pp.897-902
• /
• 2004

PSMC5 subunit, which belongs to the 26S proteasomal subunit family, plays an important role in the antigen presentation mediated by MHC class I molecular. Full-length cDNA of porcine PSMC5 was isolated using the in silico cloning and rapid amplification of cDNA ends (RACE). Amino acid was deduced and the primary structure was analyzed. Results revealed that the porcine PSMC5 gene shares the high degree of sequence similarity with its mammalian counterparts at both the nucleotide level and the amino acid level. The RT-PCR was performed to detect the porcine PSMC5 expression pattern in seven tissues and the result showed that high express level was observed in spleen, lung, marrow and liver while the low express level was in muscle. The full-length genomic DNA sequence of porcine PSMC5 gene was amplified by PCR and the genomic structure revealed that this gene was comprised by 12 exons and 11 introns. Best alignment of the cDNA and genomic exon DNA sequence presents 4 mismatches and this information potentially bears further study in gene polymorphisms.

• 한국전기전자재료학회:학술대회논문집
• /
• 한국전기전자재료학회 2008년도 하계학술대회 논문집 Vol.9
• /
• pp.143-143
• /
• 2008

Nanowires are promising options for building nanoscale electronic structures coming from high conductivity of nanowires. In particular, Deoxyribonucleic acid (DNA), which is structurally nanowire, can obtain highly ordered electronic components for nanocircuitry and/or nanodevices because of its very flexible length controllability, nanometer-size diameter, about 2 nm, and self-assembling properties. In this work, we used the method to form DNA-Nanowires (NWs) by using chemical treatment on Silicon (Si) surface, and Aminopropyl-triethoxysilane (APTES) was used as inducer of DNA sequence to modify the characteristics of Si surface. Moreover, we performed tilting technique to align DNA by the direction of flow of DNA solution. We investigated the assembly process between DNA molecules and APTES - coated Si surface according to the APTES concentration, from $1.2{\mu}\ell$ to $120{\mu}\ell$. Atomic Force Microscopy (AFM) images showed the combination rate of DNA molecules by the change of APTES concentration. As APTES concentration becomes thicker, aggregation of DNA molecules occurs, and this makes a kind of DNA networks. In this respect, we confirmed that there's a positive relationship between the concentration of APTES and the formation rate of DNA nanowires. Since there have been lots of research preceded to utilize DNA nanowires as template, so by using this positive relationship with proper alignment technique, realization of nano electronic devices with DNA nanowires might be feasible.

• 생명과학회지
• /
• 제9권4호
• /
• pp.341-347
• /
• 1999

Insects use chitinolytic enzyme to digest chitin in the exoskelton during the molting process. We have isolated and sequenced a chitinase-encoding cDNA from the silkworm, Bombyx mandarina, compared its sequenced with genes encoding chitinolytic enzymes from other sources. The insert DNA in the clone is 2,675 nucleotides long with an open reading frame of 1,695 uncletides that encodes a protein of 565 amino acids with a molecuar weight of 63.4 kDa. The 3' -untranslated region of 889 nucleotides is AT-rich and contains two putative polyadenylation signals. The N-terminal sequence of the encoded protein contains numerous hydrophobic residues characteristic of a leader peptide. The amino acid alignment revealed that the endo-$\beta$-N-acetylglucosaminidase had 83% and 97% homology with M. sexta and B. mori, respectively. The deduced amino acid had two highly conserved region at the amino acid residues 97-111 and 139-148 that were related to the existing chitinase.