• BMB Reports
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• v.39 no.2
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• pp.183-188
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• 2006

Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.3
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• pp.421-426
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• 2002

The pyruvate dehydrogenase complex (PDC), a member of $\alpha$-keto acid dehydrogenase complex, catalyzes the oxidative decarboxylation of pyruvate with the formation of $CO_2$, acetyl-CoA, NADH, and $H^+$. This complex contains multiple copies of three catalytic components including pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Two regulatory components (E1-kinase and phospho-E1 phosphatase) and functionally less-understood protein (protein X, E3BP) are also involved in the formation of the complex. In this study, we have partially cloned the gene for E3BP in human. Nine putative clones were isolated by human genomic library screening with 1.35 kb fragment of E3BP cDNA as a probe. For investigation of cloned genes, Southern blot analysis and the construction of the restriction map were performed. One of the isolated clones, E3BP741, has a 3 kb-SacI fragment, which contains 200 bp region matched with E3BP cDNA sequences. The matched DNA sequence encodes the carboxyl-terminal portion of lipoyl-bearing domain and hinge region of human E3BP. Differences between yeast E3BP and mammalian E3BP coupled with the remarkable similarity between mammalian E2 and mammalian E3BP were confirmed from the comparison of the nucleotide sequence and the deduced amino acid sequence in the cloned E3BP. Cloning of human E3BP gene and analysis of the gene structure will facilitate the understanding of the role(s) of E3BP in mammalian PDC.

• Korean Journal of Veterinary Service
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• v.32 no.1
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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.

• Korean Journal of Veterinary Service
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• v.32 no.1
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• pp.11-18
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• 2009

Porcine epidemic diarrhea virus (PEDV), an enveloped single stranded RNA virus in the family Coronaviridae, causes acute viral enteric disease in piglets. Recently outbreaks of porcine epidemic diarrhea (PED) have been rare in Europe but frequent in Asia. In Korea, the increase of PED prevalence is showing specially in postweaning pigs. The purpose of this study was to investigate nucleotide sequence of nucleocapsid protein gene of PEDV field isolates from postweaning pigs in Korea and get more information about the viruses. A total of 15 postweaing pigs clinically suspected of PEDV infection by severe watery diarrhea and dehydration were used in this study. Viral RNA was extracted from small intestines and stools of the pigs. The N gene was amplified by nested RT-PCR, purificated, sequenced, analyzed and then compared with published sequences of other PEDV strains. Three PEDVs were isolated from the suspected postweaning pigs. The N gene of three PEDV field isolates consisted of 483 nucleotides. These PEDV field isolates showed nucleotide sequence homology range from 99.6% to 95% with Chinese strains, from 99.8% to 95.2% with Korean strains, from 97.3% to 95.7% with Japanese strains and from 96.5% to 95.7% with Belgium and British strains. The encoded pritein shared range from 98.8% to 95.6% with Chinese strains, from 99.4% to 95% with Korean strains, from 97.5% to 96.3% with Japanese strains, from 95.6% to 95% with Belgium and British strains. By phylogenetic tree analysis based on nucleotide sequence, three PEDV field isolates were clustered into two groups which were Chinese isolate groups and other Korean isolate groups. These results indicated that some of PEDV field isolates prevailing in Korean postweaning pigs may be associated with those of Chinese strains and other Korean strains.

• Korean Journal of Plant Resources
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• v.31 no.5
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• pp.531-537
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• 2018

This study was carried to survey distribution of the nucleotide polymorphisms in heme-binding (HB) domain, which is highly conserved region between 1,210 and 1,240 bp of cytochrome P450, in domestic garlic cultivars. 120 garlic cultivars collected from Korea were classified into seven HB domain variation based on the nucleotide sequence of the domain. Northern type garlic cultivars, collected from Kyungpook, Chungnam, Chungpook and Kangwon province, showed 51.3% of KP2 type nucleotide sequence, 5'-TTT/GGC/GGT/GGA/CGG/AGA/ATA/TGT/CCT/GGA-3' with coding amino acid FGGGRRICPG, 13.7% of KP1, 11.3% of CP, 8.8% of CM and 5% of KW2 types. Southern type cultivars, collected from Kyungnam province, showed 52.5% of KM type nucleotide sequence, 5'-TTT/GGC/GCA/GGA/CGG/AGA/ATT/TGT/CCT/GGA-3' with coding amino acid FGAGRRICPG, 22.5% of KP2, 5.0% of KW2 and 2,5% of CP type nucleotide sequence. These results showed that Korean garlics were cultivated in highly mixed condition even in the same region.

• Journal of Aquaculture
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• v.11 no.3
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• pp.295-301
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• 1998

Since the end of the Pliocene, ancestral strains of Astyanax fasciatus have been accidently washed into different caves at the time of flooding and have lost their eyes and body pigments. Availability of this independently derived cave fish and their ancestral form within a single species provided a unique opportunity for studying the process of molecular evolution of the visual pigment gene. The nucleotide sequence comparisons of an ancestral river fish and two cave fish showed that nucleotide polymorphism of a green-like visual pigment gene between the eyed and blind form of A. fasciatus was much higher than that between the same blind form. Considering the number of nucleotide substitutions per nucleotide site and the direction of the nucleotide substitutions, more nucleotide substituions between the different forms of fish rater than the same one were probably due to more frequent mutations in the eyed river form. Nucleotide substitutions per site at the intron have been ocurred more than three times faster than those at the exon. This result indicates that the functional constraint has affected the green-like visual pigment gene of the blind cave fish although its eye sight is no longer required.

• BMB Reports
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• v.32 no.4
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• pp.399-404
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• 1999

2,3-Dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD), which catalyzes the ring meta-cleavage of 2,3-dihydroxybiphenyl, is encoded by the phnQ gene of biphenyl- and phenanthrene-degrading Pseudomonas sp. strain DJ77. We determined the nucleotide sequence of a DNA fragment of 1497 base pairs which included the phnQ gene. The fragment lncluded an open reading frame of 903 base pairs to accommodate the enzyme. The predicted amino acid sequence of the enzyme subunit consisted of 300 residues. In front of the gene, a sequence resembling an E. coli promoter was identified, which led to constitutive expression of the cloned gene in E. coli. The deduced amino acid sequence of the PhnQ enzyme exhibited 85.6% identity with that of the corresponding enzyme in Sphingomonas yanoikuyae Q1 (formerly S. paucimobilis Q1) and 22.1% identity with that of catechol 1,2,3-dioxygenase from the same DJ77 strain. PhnQ showed broader substrate preference than previously-cloned PhnE, catechol 2,3-dioxygenase. Ten amino acid residues, considered to be important for the role of extradiol dioxygenases, were conserved.

• 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.

• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.14.1-14.6
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• 2012

Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

• Journal of Microbiology and Biotechnology
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• v.10 no.2
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• pp.244-250
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• 2000

An ${\alpha}-glucosidase$ gene (aglA) from thermophilic Bacillus sp. DG0303 was cloned, sequenced, and expressed in Escherichia coli. The aglA was localized to the 2.1-kb PvuI-XmnI region within the 5.9-kb DNA insert of the gybrid plasmid pAG1. The gene consisted of an open reading frame of 1,686 bp with an unusual GTG initiation codon and TGA termination codon. The amino acid sequence deduced from the nucleotide sequence predicted a protein of 562 amino acid residues with a M, of 66,551 dalton. A comparative amino acid sequence analysis revealed that DG0303 ${\alpha}-glucosidase$ is related to bacillary oligo-1, 6-glucosidases. The Bacillus sp. DG0303 ${\alpha}-glucosidase$ showed a high sequence identity (36-59%) to the B. flavocaldarius, B. cereus, and B. thermoglucosidasius oligo-1, 6-glucosidases. The number of prolines in theses four ${\alpha}-glucosidases. was observed to increase with increasing thermostability of these enzymes. The cloned ${\alpha}-glucosidase was purified from E. coli $DH5{\alpha}$ bearing pAG1 and characterized. The recombinant enzyme was identical with the native enzyme in its optimum pH and in its molecular mass, estimated by sodium dodecy1 sulfate-polyacrylamide gel electrophoresis. The temperature optimum of the cloned ${\alpha}-glucosidase$ was lower than that of the native enzyme.