• The Korean Journal of Food And Nutrition
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• v.19 no.4
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• pp.496-501
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• 2006

This study was to isolate a bacterium producing a alkaline protease from mud flats of the west seaside of Korea and to investigate the biochemical analysis of the alkaline protease producing from the isolate. The isolate was named as Gelidibacter sp. HK-1 based on 16S rRNA sequence, Gram staining and the photograph of electron microsceope. Optimum temperature for growth and pretense production of the isolate was $25^{\circ}C$. Growth of the isolate was reached at stationary phase after 10hrs followed by inoculation. Maximum activity of protease produced from the isolate was shown after 14hrs. Optimum temperature and pH for the protease activity were $45^{\circ}C$ and pH 9, respectively. Molecular weight of the pretense was about 50KD and the partial amino acid sequence of the pretense was Ala-Try-Ala-Leu-Asn-Thr-Ser-Val-Thr-Glu-Thr-Phe-Ala-Lys. The partial amino acid sequences of the protease showed significant homology with a pretense produced from Streptomyces avermitilis.

• Food Science of Animal Resources
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• v.33 no.6
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• pp.715-722
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• 2013

Heugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 1999.10a
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• pp.74.2-74
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• 1999

• Proceedings of the Korean Biophysical Society Conference
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• 2002.06b
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• pp.14-14
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• 2002

Genome project is a research for discovering genomic information. Human genome sequence, under the title of HGP(human genome project), was drafted successfully at the end of June, 2000. And the academic world soon predicted that related research field would be activated and since then bioinformatics has been in the spotlight.(omitted)

• The Korean Journal of Mycology
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• v.28 no.1
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• pp.26-31
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• 2000

We isolated genomic clone of FVFD16 and FVFD30 gene specifically expressed during fruit body formation of Flammulina velutipes [(Curt: Fr.) Sing] and determinated the sequences. The FVFD16 gene is including two introns in open reading frame, and FVFD30 gene is including four introns. The introns were matched GT/AG rule. The FVFD16 and FVFD30 genes contained CAAT box with similarity arrange and TATA box. CT-rich region was presented before the transcription start point. FVFD30 gene is investigated that expected the most activity of CCACC arrange. The result of FVFD16 gene analysis showed 80% homology by cDNA clone that is gene family. From the results of genomic southern blot analysis, we presumed more than two copy number gene family of FVFD16 and FVFD30 gene.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.724-730
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• 2006

A sequence characterized amplified region (SCAR) marker, which was tightly linked with the A1 mating type locus in Phytophthora infestans, was developed. During the random amplified polymorphic DNA-based phylogenic studies of 33 isolates of P infestans collected from year 2002 to 2004, we found an A1 mating type-specific DNA fragment. This 573-bp DNA fragment was generated only in the genomic DNA of the A1 mating types, when OPC-5 primer was used. Based on the specific DNA sequence, we designed the primer sets for generating the A1 mating type-specific 569-bp DNA fragment. When 33 genomic DNAs of P. infestans were subjected to PCR amplification using different primer combinations, the A1 mating type-specific DNA was amplified, when LB-1F and LB-2R primers were used. The specific 569-bp DNA fragment was generated only from all 18 A1 strains, but not from 15 A2 mating type strains. These results corresponded to the mating type discriminating bioassay of 33 isolates of P. infestans. Therefore, the primer combination of LB-1F/LB2R was chosen as a SCAR marker. Overall, this study indicates that the SCAR marker could be developed into a useful tool for mating type determination of P. infestans.

• BMB Reports
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• v.29 no.1
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• pp.52-57
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• 1996

A specific DNA fragment from Korean radish (Raphanus sativus L.) was amplified by performing PCR with oligonucleotide primers which correspond to the highly conserved regions of plant peroxidases. The size of the PCR product was ca. 400 bp, as expected from the known plant peroxidase genes. Comparison of the nucleotide and deduced amino acid sequences of the PCR product to those of other plant peroxidase-encoding genes revealed that the amplified fragment corresponded to the highly conserved region I and III of plant peroxidases. By screening a genomic library of Korean radish using the amplified fragment as a probe, two positive clones, named prxK1 and prxK2, were isolated. Restriction mapping studies indicated that the 5.2 kb Sail fragment of the prxK1 clone and the 4.0 kb EcoRI fragment of the prxK2 clone encode separate isoperoxidase genes. Analyses of the promoter region of the prxK1 clone shows that putative CAAT box, CMT box, and TGA1b binding sequence (5' TGACGT) are present 718 bp upstream from the start codon.

• Molecules and Cells
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• v.24 no.1
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• pp.60-68
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• 2007

Microsatellites, also called simple sequence repeats (SSR), are very useful molecular genetic markers commonly used in crop breeding, species identification and linkage analysis. In the present study, we constructed a microsatellite-enriched genomic library of Panax ginseng, and identified 251 novel microsatellite sequences. Tri-nt repeat units were the most abundant (46.6%), followed by di-nt repeats (35.5%). The $(AG)_n$ motif was most common (23.1%), followed by the $(AAC)_n$ motif (22.3%). From the genotyping of 94 microsatellites using marker-specific primer sets, we identified 11 intraspecific polymorphic markers as well as 14 possible interspecific polymorphic markers differing between P. ginseng and P. quinquefolius. The exact allele structures of the polymorphic markers were determined and the alleles were named. This study represents the first report of the bulk isolation of microsatellites by screening a microsatellite-enriched genomic library in P. ginseng. The microsatellite markers could be useful for linkage analysis, genetic breeding and authentication of Panax species.

• Journal of Plant Biotechnology
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• v.40 no.1
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• pp.27-36
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• 2013

We isolated and functionally characterized a Dendrobium Actin1 (DmACT1) promoter that drives strong gene expression in the orchid genus Dendrobium. A genomic fragment containing the region 3227 bp upstream of the coding region of DmACT1 was obtained by inverse PCR. Detailed comparison of the full-length cDNA and genomic sequences revealed that DmACT1 has a 1374 bp first intron in the 5' UTR. However, the 5' flanking sequences upstream of the coding region showed no obvious sequence similarities compared to those of known promoters, including plant actin promoters. Serial deletion constructs of the 5' flanking region from the translation initiation codon were fused to the coding sequence of a GUS/luciferase fusion reporter to identify the regulatory elements necessary for promoter activity. Transient assays in the flowers of Dendrobium revealed that the 5' UTR-intron greatly enhanced promoter activity. Moreover, the DmACT1 promoter with its 5' UTR-intron yielded approximately 10-fold higher reporter activity than the rice Act1 promoter-intron. Our data suggest that the DmACT1 promoter with its 5' UTR-intron is a useful tool for strong expression of transgenes in Dendrobium orchids.

• Journal of Plant Biotechnology
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• v.4 no.2
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• pp.59-65
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• 2002

ADP-glucose pyrophosphorylase (AGPase) catalyzes the key regulatory step in starch biosynthesis. Two cDNA clones encoding AGPase subunits were isolated from the leaf cDNA library of Chinese cabbage (Brassica campestris L. spp. pekinensis). One was designated as BCAGPS for the small subunit and the other as BCAGPL for the large subunit. Both cDNAs have uninterrupted open reading frames deriving 57 kDa and 63 kDa polypeptides for BCAGPS and BCAGPL, respectively, which showed significant similarity to those of other dicot plants. Also, However, the deduced amino acid sequence of BCAGPL has a unique feature. That is, it contains two regions (Rl and R2) lacking in all other plant enzymes. This is the first report of BCAGPL containing Rl and R2 among plant large subunits as well as small subunits. From the genomic Southern analysis and BAC library screening, we inferred the genomic status of BCAGPS and BCAGPL gene.