• The KIPS Transactions:PartA
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• 제9A권3호
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• pp.387-398
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• 2002

As whole genome sequences of many organisms have been revealed by small-scale genome projects, the intensive research on individual genes and their functions has been performed. However on-memory algorithms are inefficient to analysis of whole genome sequences, since the size of individual whole genome is from several million base pairs to hundreds billion base pairs. In order to effectively manipulate the huge sequence data, it is necessary to use the indexed data structure for external memory. In this paper, we introduce a workbench system for analysis and visualization of whole genome sequence using string B-tree that is suitable for analysis of huge data. This system consists of two parts : analysis query part and visualization part. Query system supports various transactions such as sequence search, k-occurrence, and k-mer analysis. Visualization system helps biological scientist to easily understand whole structure and specificity by many kinds of visualization such as whole genome sequence, annotation, CGR (Chaos Game Representation), k-mer, and RWP (Random Walk Plot). One can find the relations among organisms, predict the genes in a genome, and research on the function of junk DNA using our workbench.

• The Plant Pathology Journal
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• 제22권3호
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• pp.235-238
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• 2006

Chrysanthemum stunt viroid (CSVd) induced systemic symptoms on chrysanthemum. We detected small RNAs of approximately 22 nucleotides with sequence specificity to CSVd in chrysanthemum infected with CSVd: an indication of the presence of RNA silencing. Regardless of symptom differences associated with CSVd, the small RNAs distributed similarly in amount. Small RNAs were detected with partial-length or full-length probes, indicating that they are not restricted to specific viroid regions but likely representing most of the viroid molecule.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2003년도 생물공학의 동향(XIII)
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• pp.480-484
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• 2003

A stereoselective-hydrolysing enzyme was cloned from Pseudomonas fluorescens KCTC1767 which had high enantiomeric activity toward (S)-ketoprofen ethyl ester. Analyses of typical properties resulted in low thermostability and substrate specificity. A round error-prone PCR and StEP(STaggered Extension Process) was adopted to evolute this character. As a result, the best clone 6-52 was selected which was represented to increased thermostability(40 fold) compared to wild type enzyme in $50^{\circ}C$. Additionally, specific activity toward (S)-ketoprofen ethyl ester and p-nitrophenyl derivatives improved 3 fold and 1.5 fold, respectively. DNA sequence analyses was showed some exchanged amino acid residue that was L120p, 1208v, T249A, D287H and T357A. Which the 120th's leucine substituted for proline was presumed structurally important residue concerning with catalytic activity.

• BMB Reports
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• 제29권3호
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• pp.183-191
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• 1996

DNA fragments, homologous to the dTDP-D-glucose 4,6-dehydratase gene, obtained from the genomic DNA of Streptomyces antibioticus $T\ddot{u}99$, a producer of the unusual macrolide antibiotic chlorothricin, were cloned and sequenced. This dehydratase gene was designated as oxil. The coding region of the oxil gene is composed of 987 bp, and analysis of the DNA sequence data reveals sequences for the gene products of 329 amino acids (molecular weight of 36,037). The deduced amino acids are 59% identical to the StrE, dTDP-D-glucose 4,6-dehydratase from the streptomycin pathway. The oxil's function was examined by expressing it in E. coli using the T7 RNA polymerase/promoter system (pRSET) to produce an active fusion protein including a his tag. This enzyme shows specificity of substrate, specific only to dTDP-D-glucose.

• BMB Reports
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• 제35권5호
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• pp.513-517
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• 2002

We describe a new method for identifying the sequences that signal the start of translation, and the boundaries between exons and introns (donor and acceptor sites) in human mRNA. According to the mandatory keyword, ORGANISM, and feature key, CDS, a large set of standard data for each signal site was extracted from the ASCII flat file, gbpri.seq, in the GenBank release 108.0. This was used to generate the scoring matrices, which summarize the sequence information for each signal site. The scoring matrices take into account the independent nucleotide frequencies between adjacent bases in each position within the signal site regions, and the relative weight on each nucleotide in proportion to their probabilities in the known signal sites. Using a scoring scheme that is based on the nucleotide scoring matrices, the method has great sensitivity and specificity when used to locate signals in uncharacterized human genomic DNA. These matrices are especially effective at distinguishing true and false sites.

• Journal of Microbiology and Biotechnology
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• 제25권6호
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• pp.845-855
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• 2015

The present study describes the gene cloning and high-level expression of an alkaline and thermostable lipase gene from Trichosporon coremiiforme V3. Nucleotide analysis revealed that this lipase gene has an open reading frame of 1,692 bp without any introns, encoding a protein of 563 amino acid residues. The lipase gene without its signal sequence was cloned into plasmid pPICZαA and overexpressed in Pichia pastoris X33. The maximum lipase activity of recombinant lipase was 5,000 U/ml, which was obtained in fed-batch cultivation after 168 h induction with methanol in a 50 L bioreactor. The purified lipase showed high temperature tolerance, and being stable at 60℃ and kept 45% enzyme activity after 1 h incubation at 70℃. The stability, effects of metal ions and other reagents were also determined. The chain length specificity of the recombinant lipase showed high activity toward triolein (C18:1) and tripalmitin (C16:0).

• Proceedings of the Microbiological Society of Korea Conference
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• 한국미생물학회 2003년도 International Meeting of the Microbiological Society of Korea
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• pp.118-121
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• 2003

A method for detection and quantification of aceticlastic methanogens using a real-time PCR with a TaqMan probe was developed. Two sets of primers and probes targeting the family Methanosarcinaceae and Methanosaetaceae were designed by using the Ribosormal Database Project (RDP) II, and softwares for phylogenetic probe design and sequence analysis. Target-group specificity of each set of primers and probe was verified by testing DNAs isolated from pure cultures of 28 archaeal strains purchased from DSMZ. Cell numbers in the 28 archaeal cultures and in the samples from anaerobic processes were quantified using a real-time PCR with the sets of primers and probe. In conclusion, the real-time PCR assay was very specific for the corresponding target methanogenic family and was proved to be a powerful method for quantification of aceticlastic methanogens in anaerobic processes.

• Korean Journal of Microbiology
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• 제30권6호
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• pp.488-494
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• 1992

Three clones containing mouse CD4 gene were prepared using AKR genomic cosmid library. The role of 6, 500 bp 5' flanking region of the first exon of the AKR CD4 gene in tissue or developmental stage specific expression of CD4 has been studied. The deletion constructs containing various amounts of CD4 5' flanking sequences were prepared, and they were transfected into the cell lines representing different cell types or developmental stages of CD4 expression. Study of the reporter gene expression revealed that at least 1, 700 bp of 5' flanking region did retain promoter activity for CD4 expression. This area did not seem to contain enhancer activity for a full expression of CD4. However, the putative promoter interacted with other tissue specific enhancer sequence and showed the tissue specificity of the enhancer element.

• Biomedical Science Letters
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• 제12권3호
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• pp.225-231
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• 2006

Fibrinolytic enzyme was purified from the fruiting bodies of Lepista nuda, using DEAE-Cellulose chromatography, Phenyl Sepharose chromatography, and Mono-S column chromatography. The substance has a molecular weight of 30006.62 Da as measured by MALD-TOF mass spectrometry. The N-terminal amino acid sequence of the enzyme was Tyr-Pro-Ser-Pro-Ser-His-Gln-Thr-Ala-Val-Asn-Ala-Ile-Ile-X. The activity of the enzyme was inhibited by PMSF, indicating that the enzyme is a serine protease. No inhibition was found with E-64, pepstatin, and EDTA. It has broad substrate specificity for synthetic peptides. The enzyme was stable up to $30^{\circ}C$. The enzyme hydrolyzes both Aa and y chains of human fibrinogen but did not show any reactivity for $B{\beta}$ chain of human fibrinogen.

• Proceedings of the Microbiological Society of Korea Conference
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• 한국미생물학회 2002년도 추계학술대회
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• pp.159-161
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• 2002

Bacteriophage lambda integrase carries out the site-specific recombination of lambda. Integrase contains two DNA binding domains with distinct sequence specificity, namely arm-type binding and core-type binding domains. The amino-terminal arm-binding domain is structurally related to the three-stranded $\beta-sheet$ family of DNA-binding domains. Integrase binding to the high affinity arm-type site by the amino-terminal domain facilitates Int binding to the low affinity core-type site, where the cleavage and strand exchange occurs. The amino-terminal domain of Int also modulates the core-binding and catalysis through intramolecular domain-domain interaction and/or intermolecular interactions between Int monomers. In addition, the amino-terminal domain interacts cooperatively with excisionase during excision. This indicates that amino-terminal domain of Int plays an important role in formation of proper higher-order nucleoprotein structure required for lambda site-specific recombination.