• Journal of Microbiology and Biotechnology
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• 제12권1호
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• pp.130-136
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• 2002

The internal transcribed spacer (ITS) region in the genus Tricholoma was analyzed, including for its primary nucleotide sequence and secondary structural characterization. The secondary structures of the ITS2 region in the genus Tricholoma were identified for use in bioinformatic processes to study molecular evolution and compare secondary structures. Ten newly sequenced ITS regions were added to the analysis and submitted to the GenBank database. The resulting structure from a minimum energy algorithm indicated the four-domain model, as previously suggested by others. The conserved secondary structure of the ITS2 sequences of the genus Tricholoma exhibited certain unique features, including pyrimidine tracts in the loops of domain A and a complete structure containing four domains, with motifs identified in other ITS2 secondary structures. A phylogenetic tree was derived from sequence alignment based on the secondary structures. From the resulting maximum parsimonious tree, it was found that the species in the genus Tricholoma had evolved monophyletically and were composed of four groups, as supported by the bootstrapping values and pileus color.

• 한국동물위생학회지
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• 제36권1호
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• pp.23-30
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• 2013

An avian rotavirus (AvRV-2) was isolated from feces of broilers suffering from acute gastroenteritis in 2011. It was the first avian rotavirus isolated in Korea. To investigate the molecular characteristics of AvRV-2, the VP4, VP6, VP7 and NSP4 gene nucleotide sequences were determined and compared with those of rotavirus strains available in the GenBank database. The phylogenetic tree of VP7 gene showed that AvRV-2 had a high degree of nucleotide sequence homology (93.4% to 94.7%) with those of rotaviruses belonging to genotype G19 cluster. The phylogenetic tree of the VP4 gene revealed a high degree of nucleotide sequence homology (95.8% to 95.9%) with genotype P[30] rotaviruses isolated from chickens. The VP6 and NSP4 gene nucleotide sequences showed the highest identities with those of avian strains with 95.3% to 96.4% and 90.3% to 92.2%, respectively. Genetic characterization of the VP4, VP6, VP7 and NSP4 showed that AvRV-2 strain was most closely related to chicken rotavirus strains from Germany and Japan. Comparative nucleotide sequences and phylogenetic analysis indicated that avian rotavirus isolated from broilers belonged to genotype G19P[30] and it was the first report on avian rotavirus infection in Korea.

• 전자공학회논문지B
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• 제33B권2호
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• pp.168-177
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• 1996

In this paper, we propose an on-line recognition system of chinese characters using an adaptive resonance theory-1(ART-1) neural network. Strokes, primitive components of chinese characters are usually warped into a cursive form and classifying them is very difficult. To deal with such cursive strokes, we use an ART-1 neural network that has the following advantages: (1) it automatically assembles similar patterns together to form classes in a self-organized manner: (2) it directly accesses the recognition codes corresponding to binary input patterns after self-stabilizing; (3) it doesn't tends to get trapped in local minima, or globally incorrect solutions. A database for character recognition also dynamically constructed with generalized character lists, and a new character can be included simply by adding a new sequence to the list. Character recognition is achieved by traversing the chinese datbase with a sequence of recognized strokes and positional relations between the strokes. To verify the performance of the system. We tested it for 1800 daily-used basic chinese second per character. This results suggest that the proposed system is pertinent to be put into practical use.

• Journal of Photoscience
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• 제8권3_4호
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• pp.93-97
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• 2001

Heterosigma akashiwo has been reported as red-tide causing phytoplankton in the Korean coastal area during summer when they are exposed to high light. It also shows photosynthetic adaptability to strong light during culture in the laboratory. On the basis of these observations, we tried to find out some genes specifically expressed in Heterosimga akashiwo during exposure to high light, assuming that they might have some resistant mechanisms associated with light adaptation. For this purpose, we carried out DD-PCR to detect differentially expressed mRNAs from cells that had been illuminated under high light for 3 days. We found eight cDNA clones that had been expressed specificically for high light. When they were further screened by reverse Northern hybridization, three of them were identified to be positive cDNA clones. When these cDNA fragments were subjected to DNA sequencing and then their base sequences were compared to GenBank database, one of them showed sequence homology 86% identical to the partial sequence of 16S rRNA gene of eubacterium CRO-18.

• 천문학회보
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• 제38권1호
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• pp.41.2-41.2
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• 2013

We present the statistical properties of a volume-limited sample of 7,429 nearby (z = 0.033-0.044) galaxies from the Sloan Digital Sky Survey Data Release 7. By performing a visual inspection, we classified our sample galaxies according to the Hubble sequence (Hubble 1926, 1936). Then we excluded apparently smaller and flatter galaxies from our database because morphology classification on them turned out to be difficult. Our results cover structural (e.g. concentration index, color, magnitude, stellar mass, etc.), spectroscopic (e.g. velocity dispersion, $H{\beta}$ absorption line, Fe absorption line, Mg absorption line, accretion rate, $H{\alpha}$ emission line, etc.), and environmental (e.g. density, etc.) properties of each morphology type based on morphology distribution. For this analysis, we used the recent re-measurements of spectral line strengths by Oh and collaborators (2011). Our statistics confirm the up-to-date understanding on galaxy populations, e.g., correlations between morphology and line strengths and in turn derived ages and so on.

• International Journal of Industrial Entomology and Biomaterials
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• 제25권1호
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• pp.115-121
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• 2012

The bumblebee Bombus terrestris is widely used in greenhouses to pollinate crops. Here, we report the molecular cloning and characterization of chymotrypsin inhibitor and chitin-binding protein homologs from B. terrestris. Two cDNAs encoding chymotrypsin inhibitor (Bt-CI) and chitin-binding protein (Bt-CBP) homologs were cloned from B. terrestris. Gene sequence analysis showed that Bt-CI gene consists of three exons encoding 75 amino acids, including a predicted 20-amino acid signal peptide, while Bt-CBP consists of two exons encoding 78 amino acids, including a predicted 26-amino acid signal peptide. The mature Bt-CI and Bt-CBP peptides contain ten and six conserved cysteine residues, respectively. Database searches using the deduced sequences of Bt-CI and Bt-CBP showed similarity to those from B. impatiens (96% peptide sequence identities). Bt-CI and Bt-CBP were expressed in both the venom gland and fat body of B. terrestris worker bees. The recombinant Bt-CI and Bt-CBP peptides were expressed in baculovirus-infected insect cells. Taken together, our findings describe the molecular characterization of Bt-CI and Bt-CBP from B. terrestris.

• Molecules and Cells
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• 제21권2호
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• pp.269-275
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• 2006

A recent report of the Korean Intellectual Property Office(KIPO) showed that the number of biological sequence-based patents is rapidly increasing in Korea. We present biological features of Korean patented sequences though bioinformatic analysis. The analysis is divided into two steps. The first is an annotation step in which the patented sequences were annotated with the Reference Sequence (RefSeq) database. The second is an association step in which the patented sequences were linked to genes, diseases, pathway, and biological functions. We used Entrez Gene, Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Through the association analysis, we found that nearly 2.6% of human genes were associated with Korean patenting, compared to 20% of human genes in the U.S. patent. The association between the biological functions and the patented sequences indicated that genes whose products act as hormones on defense responses in the extra-cellular environments were the most highly targeted for patenting. The analysis data are available at http://www.patome.net

• Journal of Microbiology
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• 제42권2호
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• pp.139-142
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• 2004

To identify genes involved in the decolorization of brilliant green, we isolated random mutants generated by transposon insertion in brilliant green-decolorizing bacterium, Citrobacter sp. The resulting mutant bank yielded 19 mutants with a complete defect in terms of the brilliant green color removing ability. Southern hybridization with a Tn5 fragment as a probe showed a single hybridized band in 7 mutants and these mutants appeared to have insertions at different sites of the chromosome. Tn5-inserted genes were isolated and the DNA sequence flanking Tn5 was determined. By comparing these with a sequence database, putative protein products encoded by bg genes were identified as follows: bg 3 as a LysR-type regulatory protein; bg 11 as a MalG protein in the maltose transport system; bg 14 as an oxidoreductase; and bg 17 as an ABC transporter. The sequences deduced from the three bg genes, bg 2, bg 7 and bg 16, showed no significant similarity to any protein with a known function, suggesting that these three bg genes may encode unidentified proteins responsible for the decolorization of brilliant green.

• Genomics & Informatics
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• 제11권4호
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• pp.289-291
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• 2013

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.

• 한국미생물·생명공학회지
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• 제48권4호
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• pp.480-490
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• 2020

A novel lipase gene, Lip-1420, was isolated from a metagenomic library constructed from reed marsh from Mt. Jumbong in Korea, comprising 112,500 members of recombinant plasmids. The DNA sequence of Lip-1420-subclone (5,513 bp) was found to contain at least 11 ORFs according to the GenBank database. The ORF-3 gene was inserted into the pET21a plasmid containing the C-terminal 6-His tag and transformed into E. coli BL21(DE3) to express the recombinant lipase protein. Lip-1420 was purified using a fast protein liquid chromatography system. The gene was registered in GenBank (MH628529). The values of Km and Vmax were determined as 0.268 mM and 1.821 units, respectively, at 40℃ and pH 8.0, using p-nitrophenyl palmitate as the substrate. This lipase belongs to family IV taxonomically because it has conserved HGGG and GDSAG motifs in the constitutive amino acid sequence. According to the predicted structural model, the binding sites are represented by residues H78, G81, D150, S151, A152, V181, and D236. Finally, Lip-1420 showed triolein selectivity for methanolysis between triolein (18:1) and tristearin (18:0) substrates. Further study of the selective mechanism and structure-function relationship of this new lipase could be useful for more practical applications.