• BMB Reports
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• v.44 no.10
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• pp.653-658
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• 2011

Sclerotinia sclerotiorum fungus has three endoxylanases induced by wheat bran. In the first part, a partial xylanase sequence gene (90 bp) was isolated by PCR corresponding to catalytic domains (${\beta}5$ and ${\beta}6$ strands of this protein). The high homology of this sequence with xylanase of Botryotinia fuckeliana has permitted in the second part to amplify the XYN1 gene. Sequence analysis of DNA and cDNA revealed an ORF of 746 bp interrupted by a 65 bp intron, thus encoding a predicted protein of 226 amino acids. The mature enzyme (20.06 kDa), is coded by 188 amino acid (pI 9.26). XYN1 belongs to G/11 glycosyl hydrolases family with a conserved catalytic domain containing $E_{86}$ and $E_{178}$ residues. Bioinformatics analysis revealed that there was no Asn-X-Ser/Thr motif required for N-linked glycosylation in the deduced sequence however, five O-glycosylation sites could intervene in the different folding of xylanses isoforms and in their secretary pathway.

• Journal of Microbiology
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• v.42 no.1
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• pp.56-59
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• 2004

Together with the previous reports, my computer survey revealed that several bacteria contain six copies of the type group II intron IntA. The sequence analysis of IntAs showed the high level of homology in the nucleotide sequence (91.9-99.8%). The consensus sequence, 2,270 base pair long, was derived from the nucleotide sequences of all IntA members. The size of the open reading frame intA was 502 amino acids long, that is homologous to reverse transcriptase-like proteins encoded within the group II introns. It was reported that EPEC.IntA and Sf.IntA were inserted into IS911 and IS629, respectively. The sequence of the flanking region IntA was analyzed here. The data show the insertion of EC.IntA into IS629, the insertion of EHEC.IntA into IS3, the insertion of Yp.IntA into IS904-like sequence, and the insertion of EK12.IntA into IS911. Interestingly, these IS elements nested by IntAs were the members of IS3 family elements. The sequences of the IS3 members correspond to the OrfB with the DDE motif conserved in retroviral integrases. Alignment of the flanking sequences of IntAs revealed that the flanking regions -25 to + 10 of insertion sites, that are generally believed to be required for the retrohoming, were not strongly conserved. The data presented here suggests that the retrohoming pathway of IntA seems to differ from those of other group II introns.

• Molecules and Cells
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• v.40 no.12
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• pp.954-965
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• 2017

Mammalian genomes are well established, and highly conserved regions within odorant receptors that are unique from other G-protein coupled receptors have been identified. Numerous functional studies have focused on specific conserved amino acids motifs; however, not all conserved motifs have been sufficiently characterized. Here, we identified a highly conserved 18 amino acid sequence motif within transmembrane domain seven (CAS-TM7) which was identified by aligning odorant receptor sequences. Next, we investigated the expression pattern and distribution of this conserved amino acid motif among a broad range of odorant receptors. To examine the localization of odorant receptor proteins, we used a sequence-specific peptide antibody against CAS-TM7 which is specific to odorant receptors across species. The specificity of this peptide antibody in recognizing odorant receptors has been confirmed in a heterologous in vitro system and a rat-based in vivo system. The CAS-TM7 odorant receptors localized with distinct patterns at each region of the olfactory epithelium; septum, endoturbinate and ectoturbinate. To our great interests, we found that the CAS-TM7 odorant receptors are primarily localized to the dorsal region of the olfactory bulb, coinciding with olfactory epithelium-based patterns. Also, these odorant receptors were ectopically expressed in the various non-olfactory tissues in an evolutionary constrained manner between human and rats. This study has characterized the expression patterns of odorant receptors containing particular amino acid motif in transmembrane domain 7, and which led to an intriguing possibility that the conserved motif of odorant receptors can play critical roles in other physiological functions as well as olfaction.

• Journal of the Korea Organic Resources Recycling Association
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• v.16 no.4
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• pp.64-73
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• 2008

The cDNA of CCF (coelomic cytolytic factor)-like gene (EC 3.2.1.16), a kind of glycosyl hydorlase, was isolated and cloned from the midgut of the earthworm Eisenia anderi. The size of nucleotide sequence appeared to be 1,152 bp and its predicted coding region was composed of 384 amino acid residues including the initiation methionine. The 17 residues at N-terminal end in the deduced amino acid sequence were regarded to be a signal peptide. Based on the amino acid sequence analysis, it appeared that this CCF-like protein could belong to glycosyl hydrolase family 16 (GHF16) and showed a high sequence homology of about 79~99% with CCF and CCF-like proteins from other earthworm species. The CCFs and CCF-like proteins from various earthworm species exhibited a 100% homology in the polysacchride-binding motif and glucanase motif. It has been reported that the CCFs isolated from E. fedita appeared to show a broader pattern recognition specificity than those from other earthworm species because this species resides in decaying organic matter showing very high microbial activity, implying that CCF-like protein isolated in this study from E. andrei might exhibit a broad substrate specificity that is a useful characteristic for industrial application. A phylogenetic analysis using the deduced amino acid sequences of CCF-related proteins through the BLASTX revealed that GHF16 families could be divided into three groups of metazoa, viriplantae and eubacteria subfamily. Subsequently the CCF-related proteins of metazoa subfamily could clearly be subgroup into lophotrochozoan and edysozoan type including a deuterostome origin. Further understanding of the biological properties of E. andrei CCF-like protein should be addressed to regulate the ${\beta}$-D-glucan hydrolysis and production for the industrial uses.

• Biomolecules & Therapeutics
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• v.3 no.4
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• pp.311-315
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• 1995

The K. aerogenes ureal gene product was previously shown to facilitate assembly of the crease metallocenter (Lee, M. H., Mulrooney, S. B., Renner, M. J., Markowicz, Y., and Hausinger, R. P. (1992) J. Bacteriol. 174, 4324-4330). UreG protein has now been purified and characterized. Although the protein is predicted to possess a putative NTP-binding P-loop motif, equilibrium dialysis studies showed negative results. Immunogold electron microscopic studies using polyclonal antibodies directed against UreG protein confirm that UreG is located in the cytoplasm as predicted in the DNA sequence.

• Journal of the Korean Society of International Agriculture
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• v.23 no.5
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• pp.546-551
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• 2011

Chrysanthemums, often called mums or chrysanths, belong to the genus Chrysanthemum, which includes about 30 species of perennial flowering plants in the family Asteraceae. We extracted DNA from Dendranthema grandiflorum ('Smileball') to construct a simple sequence repeat (SSR)-enriched library, using a modified biotin-streptavidin capture method. GS FLX (Genome Sequencer FLX System which provides the flexibility to perform the broad range of applications) sequencing (at the 1/8 run specification) resulted in 18.83 mega base pairs (Mbp) with an average read length of 280.06 bp. Sequence analyses of all SSR-containing clones revealed a predominance of di-nucleotide motifs (16,375, 61.5%) followed by tri-nucleotide motifs (6,616, 24.8%), tetra-nucleotide motifs (1,674, 6.3%), penta-nucleotide motifs (1,283, 4.8%), and hexa-nucleotide motifs (693, 2.6%). Among the di-nucleotide motifs, the AC/CA class was the most frequently identified (93.5% of all di-nucleotide types), followed by the GA/AG class (6.1%), the AT/TA class (0.4%), and the CG/GC class (0.03%). When we analyzed the distribution of different repeat motifs and their respective numbers of repeats, regardless of the motif class, of 100 SSR markers, we found a higher number of di-nucleotide motifs with 70 to 80 repeats; we also found two di-nucleotide motifs with 83 and 89 repeats, respectively, but their product lengths were within optimum size (297 and 300 bp). In future work, we will screen for polymorphisms of possible primer pairs. The results will provide a useful tool for assessing molecular diversity and investigating the population structure among and within Chrysanthemum species.

• Korean Journal Plant Pathology
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• v.11 no.3
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• pp.271-277
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• 1995

The RNA nucleotide sequences of the 3/-noncoding regions (3'-NCRs) of two Korean strains of turnip mosaic virus (TuMV), Ca and cqs, have been determined from their cDNA clones that encompassed the 3'-terminal regions of the viral genomic RNAs. The 3'-NCRs of both strains were 209 nucleotides long, terminated with GAC residues and poly (A) tails. The potential polyadenylational signal motif, UAUGU, was located 140 nucleotides upstream from the poly (A) tail in each of the virus. A highly conserved hexanucleotide sequence [A G U G A/U G/C], which was common in the 3'-NCRs of the potyvirus RNAs, was also found at the regions of 119 bases upstream from the 3'-end. Comparison of the 3'-NCRs of the two Korean isolates with those of four strains from Canada, China and Japan showed significantly identical genotypes (94.3∼99.5%). The secondary structure of three loops with long stems was found within the 3'-NCRs by sequence analysis. The substituted bases in the region among the six TuMV strains did not alter their secondary structures. Length of the 3'-NCRs of the know 11 potyviral RNAs and TuMV RNAs was different from one another and their nucleotide sequences showed 55.7% to 24.0% of homology. The 3'-NCR, therefore, is considered to be useful for phylogenetic studies in potyviruses.

• Proceedings of the KSRS Conference
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• v.2
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• pp.627-630
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• 2006

Sequential Pattern Mining is the mining approach which addresses the problem of discovering the existent maximal frequent sequences in a given databases. In the daily and scientific life, sequential data are available and used everywhere based on their representative forms as text, weather data, satellite data streams, business transactions, telecommunications records, experimental runs, DNA sequences, histories of medical records, etc. Discovering sequential patterns can assist user or scientist on predicting coming activities, interpreting recurring phenomena or extracting similarities. For the sake of that purpose, the core of sequential pattern mining is finding the frequent sequence which is contained frequently in all data sequences. Beside the discovery of frequent itemsets, sequential pattern mining requires the arrangement of those itemsets in sequences and the discovery of which of those are frequent. So before mining sequences, the main task is checking if one sequence is a subsequence of another sequence in the database. In this paper, we implement the subsequence matching method as the preprocessing step for sequential pattern mining. Matched sequences in our implementation are the normalized sequences as the form of number chain. The result which is given by this method is the review of matching information between input mapped sequences.

• Journal of Microbiology
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• v.35 no.3
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• pp.206-212
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• 1997

Heliobacillus mobilis is a strictly anaerobic Gram-positive bacterium which contains a primitive Photosystem I-type reaction center. The membrane-bound cytochrome $C_{553}$ from the heliobacterium suggested to be the immediate electron donor to the photooxidized pigment (P798+) has been isolated and characterized. The heme protein was visualized as a major component with an apparent molecular size of 17kDa in TMBZ-staining analysis of the membrane preparation and showed characteristic $\alpha$ (552.5 nm), $\beta$ (522nm), and Soret absorption (416 nm) peaks of a typical reduced c-type cytochrome in the partially purified sample. The internal 43 amino acid sequence of the electron donor was obtained by chemical agent and protease treatments followed by N-terminal sequencing of the resulting fragments. The internal sequence carries lots of lysine residues and a Cys-X-X-Cys-His sequence motif which are the characteristics of typical c-type cytochromes. The analysis of the sequence by FAST or FASTA program, however, did not show any significant similarity to other known heme proteins.

• Korean Journal of Remote Sensing
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• v.22 no.5
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• pp.457-462
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• 2006

Sequential Pattern Mining is the mining approach which addresses the problem of discovering the existent maximal frequent sequences in a given databases. In the daily and scientific life, sequential data are available and used everywhere based on their representative forms as text, weather data, satellite data streams, business transactions, telecommunications records, experimental runs, DNA sequences, histories of medical records, etc. Discovering sequential patterns can assist user or scientist on predicting coming activities, interpreting recurring phenomena or extracting similarities. For the sake of that purpose, the core of sequential pattern mining is finding the frequent sequence which is contained frequently in all data sequences. Beside the discovery of frequent itemsets, sequential pattern mining requires the arrangement of those itemsets in sequences and the discovery of which of those are frequent. So before mining sequences, the main task is checking if one sequence is a subsequence of another sequence in the database. In this paper, we implement the subsequence matching method as the preprocessing step for sequential pattern mining. Matched sequences in our implementation are the normalized sequences as the form of number chain. The result which is given by this method is the review of matching information between input mapped sequences.