• Microbiology and Biotechnology Letters
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• v.23 no.2
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• pp.150-155
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• 1995

Carboxypeptidase Z(CPZ) cDNA of Absidia zychae was experssed in Saccharomyces cerevisiae. The expressed CPZ(YCPZ) was secreted about 30 mg/l into the medium and has a little higher molecular weight than the wild type CPZ in SDS-PAGE. By the result of N-terminal amino acid sequencing, YCPZ has additional 15 amino acids residues in N-terminus of CPZ. But YCPZ shows no difference with CPZ in enzyme activity and substrate specificity. For the identification of processing mechanism of YCPZ, 36-Arg was changed to 36-Thr by site specific mutagenesis. Mutant YCPZ does not processed at 36-Thr. It was, therefore, concluded that the YCPZ was processed by KEX2. According to endo F treatment, high amount of carbohydrate was N-glycosylated in YCPZ.

• Journal of the Korean Society of Tobacco Science
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• v.21 no.2
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• pp.152-159
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• 1999

A CAB cDNA clone(pKGCAB) encoding the light harvesting chlorophyll a/b binding protein of the semi-shade plant, Korean ginseng(Panax ginseng C. A. Meyer) was isolated by the one-way path random sequencing of ginseng cDNA library clones and transgenic tobacco plants(Nicotiana tabacum NC82) were produced by the transformation of this ginseng CAB gene in use of Agrobacterium tumefaciens LBA4404. The CAB gene showed type 1 structure of LHCP-II, 84% similarity in nucleotide sequence and 92% in amino acid sequence to that of Nicotiana tabacum CAB40, respectively. Seed germination and initial growth of the transgenic tobacco plants transformed with the cDNA fragment were accelerated under low light intensity compared with those of normal tobacco plant, that may result from the higher light sensitivity of the transgenic plants than that of the normal.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.45-52
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• 2000

Genomic approach produces massive amount of data within a short time period, New high-throughput automatic sequencers can generate over a million nucleotide sequence information overnight. A typical DNA chip experiment produces tens of thousands expression information, not to mention the tens of megabyte image files, These data must be handled automatically by computer and stored in electronic database, Thus there is a need for systematic approach of data collection, processing, and analysis. DNA sequence information is translated into amino acid sequence and is analyzed for key motif related to its biological and/or biochemical function. Functional genomics will play a significant role in identifying novel drug targets and diagnostic markers for serious diseases. As an enabling technology for functional genomics, bioinformatics is in great need worldwide, In Korea, a new functional genomics project has been recently launched and it focuses on identi☞ing genes associated with cancers prevalent in Korea, namely gastric and hepatic cancers, This involves gene discovery by high throughput sequencing of cancer cDNA libraries, gene expression profiling by DNA microarray and proteomics, and SNP profiling in Korea patient population, Our bioinformatics team will support all these activities by collecting, processing and analyzing these data.

• Journal of Microbiology and Biotechnology
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• v.13 no.2
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• pp.236-242
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• 2003

A culture-independent and -dependent survey of the bacterial community structure in the rhizosphere and soil samples from hot pepper plants was conducted using 16S rDNA clone library and FAME analyses. Out of the 78 clones sequenced, 56% belonged to Proteobacteria, 4% to high G+C Gram- positive group, 3% to Cytophyga-Flexibacter-Bacreroides, and 32% could not be grouped with any known taxonomic division. Among the 127 FAME isolates identified, 66% belonged to low G+C Gram-positive bacteria (Baciilus spp.) and 26% to high G+C Gram-positive bacteria. In a cluster analysis, the results for both methods were found to be strikingly dissimilar. The current study is the first comparative study of FAME and 165 rDNA clonal analyses performed on the same set of soil, rhizosphere soil, and root samples.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.7
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• pp.955-961
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• 2009

The aim of this study was to determine the specific polymorphic sites in cattle breeds and inter- and interbreed genetic variation among breeds and to develop a databank of Turkish native cattle mtDNA using sequence analysis. The entire D-loop region was analyzed based on DNA sequences in Turkish Grey, East Anatolian Red, South Anatolian Red, and Anatolian Black native breeds. In total, 68 nucleotide differences were observed at 26 different sites. The variable positions consisted of 22 transitions, two transversions, and two insertions, but no deletions. Haplotype number, haplotype diversity, nucleotide diversity, and mean number of pairwise difference values were found to be 17, 0.993, 0.00478, and 4.275, respectively. In addition, a phylogeny was developed by comparison among cattle populations for which the entire D-loop sequence was available. A high level of genetic variation was observed within and among the native cattle breeds.

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.3
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• pp.159-163
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• 2000

The genome sequencing project has generated and will contitute to generate enormous amounts of sequence data. Since the first complete genome sequence of bacterium Haemophilus in fluenzae was published in 1995, the complete genome sequences of 2 eukaryotic and about 22 prokaryotic organisms have detemined. Given this everincreasing amounts of sequence information, new strategies are necessary to efficiently pursue the phase of the geome project- the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip technology was developed to efficienfly identify the differential expression pattern of indepondent biogical samples. DNA chip provides a new tool for genome expreesion analysis that may revolutionize revolutionize many aspects of human kife including mew surg discovery and human disease diagnostics.

• Korean Journal of Medicinal Crop Science
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• v.17 no.1
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• pp.26-32
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• 2009

The region containing 18S rRNA gene, ITS 1 and part of the 5.8S rRNA gene of the Atractylodes japonica Koidz was amplified by PCR and the product cloned in a pBluescript SK II plasmid. DNA sequence of the cloned DNA was determined and submitted to the GenBank (accession number EU678363). Phylogenetic analysis of the ITS 1 DNA showed close similarity with the other plant species of the family Compositae. The extract of the plant materials of five different members of the family Compositae was analyzed by HPLC to detect atractylon. Extract of the A. japonica Koidz showed presence of significant amount of atractylon. However, noticeable amount of atractylon was not detected by the same analyses from the extracts of the other plants belonging to the family Compositae including Artemisia capillaris, Chrysantemum zawadskii, Eclipta prostrata or Taraxacum platycarpum.

• Animal cells and systems
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• v.4 no.3
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• pp.257-261
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• 2000

To elucidate phylogenetic relationships among poecilostome families 18S rDNA sequence data were generated for seven poecilostome and one cyclopoid copopods by PCR cloning and sequencing techmiques. Phylogenetic trees were constructed by maximum parsimony, neighbor joining, and maximum likelihood methods using cyclopoid sequence as an outgroup. The results from three different analyses showed that the seven poecilostome families were eiridel into two groups: Clausidiidae-Myicolidae-Synaptiphillidae-bomolochidae and Lichomologidae-Chondracanthidae-Ergasilidae. The molecular phylogenies were consistent with those from the morphological characters. Therefore, these analyses porvide further evidence for the utility of 18S rDNA sequences in addressing phylogenetic relationships among poecilostome families.

• Archives of Pharmacal Research
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• v.27 no.7
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• pp.776-780
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• 2004

Interferons are cytokines that confer resistance to viral infection and inhibit cellular proliferation. The interferon alpha gene from human blood samples was amplified, cloned and expressed in E. coli (BL21). Leukocyte chromosomal DNA was used as a source of template DNA. Using specific primers, the gene for HulFN$\{alpha}$-2b was amplified and inserted into the E. coli vector, pET21b, by ligation of the HindIII and BamHI linkers of the vector and insert. The insert was further analyzed by PCR, DNA restriction mapping and sequencing, and expressed in a suitable E. coli strain. The production of this important cellular protein in the laboratory has significant applications in production of the recombinant pharmaceutical proteins.

• Genomics & Informatics
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• v.18 no.1
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• pp.3.1-3.8
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• 2020

Patient-derived xenograft (PDX) mouse models are frequently used to test the drug efficacy in diverse types of cancer. They are known to recapitulate the patient characteristics faithfully, but a systematic survey with a large number of cases is yet missing in lung cancer. Here we report the comparison of genomic characters between mouse and patient tumor tissues in lung cancer based on exome sequencing data. We established PDX mouse models for 132 lung cancer patients and performed whole exome sequencing for trio samples of tumor-normal-xenograft tissues. Then we computed the somatic mutations and copy number variations, which were used to compare the PDX and patient tumor tissues. Genomic and histological conclusions for validity of PDX models agreed in most cases, but we observed eight (~7%) discordant cases. We further examined the changes in mutations and copy number alterations in PDX model production and passage processes, which highlighted the clonal evolution in PDX mouse models. Our study shows that the genomic characterization plays complementary roles to the histological examination in cancer studies utilizing PDX mouse models.