• The Journal of Korean Society of Virology
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• v.30 no.1
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• pp.71-81
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• 2000

We have determined and analyzed the full-length cDNA sequence of a coxsackievirus B3 (CVB3) Korean isolate (CVB3-Korea/97) which has been known as a general human pathogen. The whole genome contains 7,400 nucleotides and has a single large open reading frame with 6,555 nucleotides that encodes a potential polyprotein precursor of 2,185 amino acids. The genome also contains a 5' non-coding region (NCR) of 741 bases and a 3' NCR of 104 bases followed by poly(A) tail. Sequence homologies of nucleotides and deduced amino acids between the CVB3-Korea/97 strain and the prototype (Nancy strain) were 81.7% and 91.5%, respectively. The genes encoding the functional proteins including viral protease and RNA dependent RNA polymerase showed higher homology than those encoding the structural proteins. We have further analyzed the sequences of 5' NCR, VP1 and VP2 of CVB3-Korea/97, which are known as cardiovirulent determining factors at the nucleotide and amino acid levels. Although the CVB 3-Korea/97 strain was isolated from an aseptic meningitis patient without cardiomyopathy, its 234th nucleotide and 165th amino acid were uracil and Asn as same as those of other cardiovirulent strains one. However, the 155th amino acid of VP1, which closely associated with cardiovirulence, was replaced with $Arg^{155}$ by single nucleotide substitution from $A^{2916}$ to $T^{2916}$. Moreover, additional amino acid substitutions were observed in the flanking region of $Asp^{155}$. Taken together, amino acid(s) substitution in VP1 may playa critical role in determining cardiovirulence of the CVB3-Korea/97 strain rather than individual nucleotide replacements in the 5' NCR and/or an amino acid substitution in VP2.

• Clinical and Experimental Pediatrics
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• v.52 no.4
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• pp.476-480
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• 2009

Purpose : The purpose of this study was to investigate the polymorphisms of the TNF-alpha promotor gene, its susceptibility to Kawasaki disease (KD) and to assess whether the TNF-alpha promotor gene polymorphism was related the risk of coronary artery lesions (CALs). Methods : From January 2003 to January 2007, 51 children (30 boys and 21 girls) with KD and 48 children forming an age-matched control group were studied. DNA from the peripheral blood of all the children was sampled, and the DNA polymorphisms of the 5' flanking regions of the TNF-alpha promoter gene at position -308 [guanine (G) to adenine (A)] were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Then, the relationship between KD and the TNF-alpha promotor gene polymorphisms was evaluated. Results : The A allele frequency of the -308 site of the TNF-alpha promotor gene was 17.6% (9/51) for children with KD and 6.8% (3/48) for the control group children, but this result was not statistically significant. Twenty-four patients experienced CALs within 60 days after the onset of symptoms. KD children with TNF-alpha -308 A allele had lower frequencies of CALs (12.5% versus 22.2%, P>0.05). Conclusion : The DNA polymorphism of the -308 site TNF-alpha gene was not associated with susceptibility to KD and a risk of CALs. Multicenter, large-scale randomized controlled trials are needed for further study.

• Korean Journal of Ichthyology
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• v.19 no.4
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• pp.266-273
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• 2007

Heat shock proteins (HSPs) are a family of highly conserved proteins playing an important role in the functioning of unstressed and stressed cells. The HSP70 family, the most widely studied of the hsps, is constitutively expressed (hsc70) in unstressed cells and is also induced in response to stressors (hsp70), especially those affecting the protein machinery. The HSP/HSC70 proteins act as molecular chaperones and are crucial for protein functioning, including folding, intracellular localization, regulation, secretion, and protein degradation. Here, we report the identification and characterization of the putative amino acid sequence deduced from one cDNA clone identified as heat shock protein 70. The alignment showed that the putative sequence is 100% identical to the heat shock protein 70 cognate (HSC 70) of olive flounder. The 5'-flanking region sequence (approximately 1 kb) ahead of the hsc70 gene was cloned by genome walking and a putative core promoter region and transcription elements were identified. We characterized the promoter of the olive flounder hsc70 gene by examining the ability of 5'-upstream fragments to drive expression of green fluorescent protein (GFP) in live embryos.

• Journal of Microbiology and Biotechnology
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• v.14 no.2
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• pp.302-311
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• 2004

Comamonas testosteroni (formerly Pseudomonas sp.) NCIMB 10643 can grow on biphenyl and alkylbenzenes $(C_2-C_7)$ via 3-substituted catechols. Thus, to identify the genes encoding the degradation, transposon-mutagenesis was carried out using pAG408, a promoter-probe mini-transposon with a green fluorescent protein (GFP), as a reporter. A mutant, NT-1, which was unable to grow on alkylbenzenes and biphenyl, accumulated catechols and exhibited an enhanced expression of GFP upon exposure to these substrates, indicating that the gfp had been inserted in a gene encoding a broad substrate range catechol 2,3-dioxygenase. The genes (2,826 bp) flanking the gfp cloned from an SphI-digested fragment contained three complete open reading frames that were designated bphCDorfl. The deduced amino acid sequences of bphCDorfl were identical to 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC), 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (BphD), and OrfI, respectively, that are all involved in the degradation of biphenyl/4-chlorobiphenyl (bph) by Ralstonia oxalatica A5. The deduced amino acid sequence of the orfl revealed a similarity to those of outer membrane proteins belonging to the OmpW family. The introduction of the bphCDorfl genes enabled the NT-l mutant to grow on aromatic hydrocarbons. In addition, PCR analysis indicated that the DNA sequence and gene organization of the bph operon were closely related to those in the bph operon from Tn4371 identified in strain A5. Furthermore, strain A5 was also able to grow on a similar set of alkylbenzenes as strain NCIMB 10643, demonstrating that, among the identified aromatic hydrocarbon degradation pathways, the bph degradation pathway related to Tn4371 was the most versatile in catabolizing a variety of aromatic hydrocarbons of mono- and bicyclic benzenes.

• Reproductive and Developmental Biology
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• v.36 no.1
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• pp.7-12
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• 2012

DNA methyltransferase 1 (Dnmt1) gene contains three different isoform transcripts, Dnmt1s, Dnmt1o, and Dnmt1p, are produced by alternative usage of multiple first exons. Dnmt1o is specific to oocytes and preimplantation embryos, whereas Dnmt1s is expressed in somatic cells. Here we determined that porcine Dnmt1o gene had differentially methylated regions (DMRs) in 5'-flanking region, while those were not found in the Dnmt1s promoter region. The methylation patterns of the porcine Dnmt1o/Dnmt1s DMRs were investigated using bisulfite sequencing and pyrosequencing analysis through all preimplantation stages from one cell to blastocyst stage in in vivo or somatic cell nuclear transfer (SCNT). The Dnmt1o DMRs contained 8 CpG sites, which located in -640 bp to -30 bp upstream region from transcription start site of the Dnmt1o gene. The methylation status of 5 CpGs within the Dnmt1o DMRs were distinctively different at each stage from one-cell to blastocyst stage in the $in$ $vivo$ or SCNT, respectively. 55.62% methylation degree of the Dnmt1o DMRs in the $in$ $vivo$ was increased up to 84.38% in the SCNT embryo, moreover, $de$ $novo$ methylation and demethylation occurred during development of porcine embryos from the one-cell stage to the blastocyst stage. However, the DNA methylation states at CpG sites in the Dnmt1s promoter regions were hypomethylated, and dramatically not changed through one-cell to blastocyst stage in the $in$ $vivo$ or SCNT embryos. In the present study, we demonstrated that the DMRs in the promoter region of the porcine Dnmt1o was well conserved, contributing to establishment and maintenance of genome-wide patterns of DNA methylation in early embryonic development.

• Journal of Life Science
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• v.20 no.5
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• pp.655-661
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• 2010

To elucidate the mechanism underlying the suppressive regulation of hST8Sia I expression in retinoic acid (RA)-induced SK-MEL-2 cells, we characterized the promoter region of the hST8Sia I gene. Functional analysis of the 5‘-flanking region of the hST8Sia I gene by the transient expression method showed that the -1146 to -646 region, which contains putative binding sites for transcription factors c-Ets-1, CREB, AP-1 and NF-kB, functions as the RA-repressive promoter in SK-MEL-2 cells. Site-directed mutagenesis and ChIP analyses indicated that the NF-kB binding site at -731 to -722 is crucial for the RA-induced repression of hST8Sia I in SK-MEL-2 cells. In addition, the transcriptional activity of hST8Sia I suppressed by RA in SK-MEL-2 cells was strongly inhibited by extracellular signal-regulated protein kinase (ERK) inhibitor U0126 and protein kinase C (PKC) inhibitor GO6976, as determined by RT-PCR and luciferase assay of hST8Sia I promoter containing the -1146 to -646 regions. These results suggest that RA markedly modulates transcriptional regulation of hST8Sia I gene expression through the PKC/ERK signal pathway in SK-MEL-2 cells.

• Molecules and Cells
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• v.40 no.2
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• pp.100-108
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• 2017

Cathepsin F, which is encoded by CTSF, is a cysteine proteinase ubiquitously expressed in several tissues. In a previous study, novel transcripts of the CTSF gene were identified in the crab-eating monkey deriving from the integration of an Alu element-AluYRa1. The occurrence of AluYRa1-derived alternative transcripts and the mechanism of exonization events in the CTSF gene of human, rhesus monkey, and crabeating monkey were investigated using PCR and reverse transcription PCR on the genomic DNA and cDNA isolated from several tissues. Results demonstrated that AluYRa1 was only integrated into the genome of Macaca species and this lineage-specific integration led to exonization events by producing a conserved 3' splice site. Six transcript variants (V1-V6) were generated by alternative splicing (AS) events, including intron retention and alternative 5' splice sites in the 5' and 3' flanking regions of CTSF_AluYRa1. Among them, V3-V5 transcripts were ubiquitously expressed in all tissues of rhesus monkey and crab-eating monkey, whereas AluYRa1-exonized V1 was dominantly expressed in the testis of the crab-eating monkey, and V2 was only expressed in the testis of the two monkeys. These five transcript variants also had different amino acid sequences in the C-terminal region of CTSF, as compared to reference sequences. Thus, species-specific Alu-derived exonization by lineage-specific integration of Alu elements and AS events seems to have played an important role during primate evolution by producing transcript variants and gene diversification.

• Korean Journal of Microbiology
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• v.32 no.3
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• pp.215-221
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• 1994

The complete nucleotide sequence of the cloned pga gene encoding the penicillin G acylase of Bacillus megaterium ATCC 14945 and its 5'- and 3'-flanking regions was determined. The sequence revealed only one large open reading frame (2,406 hp) of the penicillin G acylase (pga) gene. Upstream from ATG of the pga gene, there was a putative ribosome binding site, Shine-Dalgarno sequence. The promoter-like structure, - 10 and - 35 sequences, was also found. Following the stop codon, TAG, a structure reminiscent of the E. coli rho-independent transcription terminator was present. The amino acid sequence was deduced from the nucleotide sequence. The molecular mass of the polypeptide was 91,983 Da. There was a potential signal sequence in its amino-terminal region. A comparison of its deduced amino acid sequence with other characterized penicillin G acylases and the result of SDS-polyacrylamide gel electrophoresis of the purified enzyme showed that a precursor polypeptide of 92 kDa was processed into two dissimilar ${\alpha}$ and ${\beta}$-subunits of 25 and 61 kDa.

• Journal of Animal Science and Technology
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• v.50 no.2
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• pp.177-184
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• 2008

Acid-labile subunit(ALS) is a 85-kDa glycosylated plasma protein which forms a 150-kDa ternary complex with 7.5-kDa insulin-like growth factor(IGF) and 40~45-kDa IGF-binding protein-3. In a previous study, the present authors prepared a porcine ALS(pALS) expression construct by inserting a pALS coding sequence into a plasmid vector following synthesis of the sequence by reverse transcription-polymerase chain reaction(RT-PCR). The expression construct, however, was subsequently found to have a mis-sense mutation at two bases of the pALS coding sequence which is presumed to have occurred through a PCR error. In the present study, the correct coding sequence was synthesized by the site-directed mutagenesis and inserted into the pET-28a(+) plasmid expression vector containing the His-tag sequence flanking the last codon of the insert DNA. After induction of the expression construct in E. coli BL21(DE3) cells, the resulting presumptive recombinant peptide was purified by the Ni-affinity chromatography. Upon SDS- PAGE, the affinity-purified peptide was resolved as a single band at a 66-kDa position which is consistent with the expected molecular mass of the presumptive recombinant pALS. Collectively, results indicate that a recombinant pALS peptide was successfully expressed and purified in the present study.

• Korean Journal of Animal Reproduction
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• v.26 no.2
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• pp.87-94
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• 2002

This study was performed during the four seasons for the production of transgenic pigs containing the Cellulase Digest Gene. Purebred Landrace gilts and sows approximately 8∼15 months of age (n=126) were used for the collection of 1-cell zygotes for DNA microinjection and transfer. Retrospectively, estrus synchronization and superovulation schemes were evaluated to assess practicality fur zygote collection. Synchronization and superovulation procedures were used that cyclic gilts were synchronized with 20mg altrenogest (ALT) per day for 9 days after PG600 administration followed by superovulation with 1000 IU pregnant mares serum gonadotropin (PMSG) and 750IU human chorionic gonadotrophin (hCG). The cellulase digestion gene for microinjection is rat elasterase promoter (rEl) linked to CelD gene. After hormone treatment, 1,422 embryos were collected from 91 donors and 95.6% (1,359/1,422) embryos were in 1-cell stage which can be visualized the pronuclei for DNA microinjection. A total of 725 DNA microinjected embryos transferred into 35 recipients and produced 65 piglets from 13 litters. Pregnancy rate according to the number of transferred embryos to recipients was higher the group which received 21 to 24 embryos (50.0%) than other groups 20.0% in less and 33.3% in more. A tail tissue was collected from 65 piglets for biopsy. PCR screening was performed on each DNA sample using two separate sets of primers specific for the 5'- and 3'-flanking region of the rEl-CelD gene. Five of the 65 piglets (7.69%) were positive for the transgene. This study provide useful information regarding production of transgenic pig for bioreactor research.