• Animal cells and systems
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• v.6 no.1
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• pp.81-84
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• 2002

SINE-R retroposons have been derived from human endogenous retrovirus HERV-K family and found to be hominoid specific. Both SINE-R retroposons and HERV_K family are potentially capable of affecting the expression of closely located genes. Using the genomic DNA from patients with schizophrenia, we identified 26 SINE-R retroposons and analyzed them with the sequences derived from the hominoid primates. The SINE-R retroposons from schizophrenia showed 89.7-96.6％ sequence similarities with the sequence of the schizo-cDNA clone that derived from postmortem tissue from the frontal cortex of an individual suffering from schizophrenial. Phylogenetic analysis using the neighbor-joining method revealed that the new SINE-R retroposons in schizophrenia have proliferated independently during hominid evolution. Such retroposons have great relevance to genomic change connected to human diseases. The data suggest that new SINE-R retroposons identified in schizophrenia deserve further investigation as potential leads on the understanding of neuropsychiatric diseases.

• Journal of Microbiology and Biotechnology
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• v.7 no.2
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• pp.157-159
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• 1997

A 340-bp chitin synthase gene(CHS) fragment was cloned from the genomic DNA of Pyricularia oryzae using a PCR process with two primer DNAs corresponding to highly conserved sequences within fungal CHS genes. The entire DNA nucleotide sequences of the cloned DNA fragment were determined and analyzed. The amino acid sequences deduced from the nucleotide sequence of the amplified DNA fragment showed 86% homology to that of the Aspergillus fumigatus CHSE gene (9). Using this PCR-amplified DNA, about 2.3 kb of including the PCR fragment of CHSE gene was cloned from genomic library.

• Korean Journal Plant Pathology
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• v.13 no.2
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• pp.113-117
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• 1997

Low moleuclar weight (LMW) RNAs were isolated form Korean peonies which expressed symptoms of stunt and epinasty. The LMW plant RNAs were purified by Qiagen column chromatography which could separate viroid specific nucleic acid at differential salt concentration. After the inoculation of the purified RNAs from the peonies, the inoculated tomatoes (cv. Rutgers) expressed the symptoms of stunt and epinasty. Also the same molecular weight RNAs with viroid-like RNAs were isolated from the inoculated tomatoes. Double-stranded cDNA were synthesized by the methods of reverse transcription (RT) and polymerase chain reaction (PCR) with the purified RNA and primers. The same cDNAs associated with viroid-like RNAs wre cloned from the inoculated tomatoes. The cDNA has been sequenced and its 375-nucleotides were arranged into secondary structure. The cloned cDNA showed 47~54% homology compared with other viroids. The sequence homology of the cloned cDNA were partially high with plant genomic RNAs.

• Journal of Preventive Medicine and Public Health
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• v.40 no.2
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• pp.102-107
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• 2007

Human Genome Project (HGP) could unveil the secrets of human being by a long script of genetic codes, which enabled us to get access to mine the cause of diseases more efficiently. Two wheels for HGP, bioinformatics and high throughput technology are essential techniques for the genomic medicine. While microarray platforms are still evolving, we can screen more than 500,000 genotypes at once. Even we can sequence the whole genome of an organism within a day. Because the future medicne will focus on the genetic susceptibility of individuals, we need to find genetic variations of each person by efficient genotyping methods.

• Genomics & Informatics
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• v.16 no.4
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• pp.27.1-27.6
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• 2018

The non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect of the primary DNA sequence on the epigenomic landscape across a 200-base pair of genomic units by integrating 127 publicly available ChromHMM BED files from the Roadmap Genomics project. Nucleotide frequency profiles of 127 chromatin annotations stratified by chromatin variability were analyzed and integrative hidden Markov models were built to detect Markov properties of chromatin regions. Our aim was to identify the relationship between DNA sequence units and their chromatin variability based on integrated ChromHMM datasets of different cell and tissue types.

• Proceedings of the Microbiological Society of Korea Conference
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• 2001.11a
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• pp.131-137
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• 2001

• Proceedings of the Zoological Society Korea Conference
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• 1994.10a
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• pp.185.2-185
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• 1994

No Abstract, See Full Text

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2001.06a
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• pp.77-80
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• 2001

A variety of different methods to generate diverse proteins, including random mutagenesis and recombination, are currently available, and most of them accumulate the mutations on the target gene of a protein, whose sequence space remains unchanged. On the other hand, a pool of diverse genes, which is generated by random insertions, deletions, and exchange of the homologous domains with different lengths in the target gene, would present the protein lineages resulting in new fitness landscapes. Here we report a method to generate a pool of protein variants with different sequence spaces by employing green fluorescent protein (GFP) as a model protein. This process, designated functional salvage screen (FSS), comprises the following procedures： a defective GFP template expressing no fluorescence is firstly constructed by genetically disrupting a predetermined region(s) of the protein, and a library of GFP variants is generated from the defective template by incorporating the randomly fragmented genomic DNA from E. coli into the defined region(s) of the target gene, followed by screening of the functionally salvaged, fluorescence-emitting GFPs. Two approaches, sequence-directed and PCR-coupled methods, were attempted to generate the library of GFP variants with new sequences derived from the genomic segments of E. coli. The functionally salvaged GFPs were selected and analyzed in terms of the sequence space and functional property. The results demonstrate that the functional salvage process not only can be a simple and effective method to create protein lineages with new sequence spaces, but also can be useful in elucidating the involvement of a specific region(s) or domain(s) in the structure and function of protein.

• Biomedical Science Letters
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• v.10 no.2
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• pp.65-73
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• 2004

I report that single-stranded antisense as a part of large circular (LC-) genomic DNA of recombinant M13 phage exhibits enhanced stability, sequence specific antisense activity, and no need for target site search. A cDNA fragment (708 bp) of rat TNF-$\alpha$ was inserted into a phagemid vector, and TNF-$\alpha$ antisense molecules (TNF$\alpha$-LCAS) were produced as single-stranded circular DNA. When introduced into a rat monocyte/macrophage cell line, WRT7/P2, TNF$\alpha$-LCAS was able to ablate LPS-induced TNF-$\alpha$ mRNA to completion. The antisense effect of TNF$\alpha$-LCAS was shown to be sequence-specific because expressions of three control genes ($\beta$-actin, GAPDH and IL-1$\beta$) were not significantly altered by the antisense treatment. Further, TNF$\alpha$-LCAS was found to be highly efficacious as only 0.1 $\mu$g (0.24 nM) of TNF$\alpha$-LCAS was sufficient to block TNF-$\alpha$ expression in 1$\times10^5$ WRT7/P2 cells. I have also observed specific antisense activity in reduction of NF-$\kappa$B gene expression. The results suggest that an antisense sequence as a part of single-stranded circular genomic DNA has a specific antisense activity.

• BMB Reports
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• v.34 no.3
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• pp.262-267
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• 2001

A cDNA coding alkaline phosphatase (AP) homologue was isolated from a cDNA library of Schizosaccharomyces pombe by colony hybridization. The nucleotide sequence of the cloned cDNA appeared to lack the N-terminal coding region. The genomic DNA encoding alkaline phosphatase homologue was isolated from S. pombe chromosomal DNA using PCR. The amplified DNA fragment was ligated into plasmid pRS315 to generate the recombinant plasmid pSW20. The DNA insert was subcloned as two smaller fragments for nucleotide sequencing. The sequence contains 2,789 by and encodes a protein of 532 amino acids with a molecular mass of 58,666 daltons. The S. pombe cells containing plasmid pSW20 showed much higher AP activity compared with the yeast cells with vector only This indicates that the cloned AP gene apparently encodes AP The predicted amino acid sequence of the S. pombe AP shares homology with those of other known APs.