• 한국작물학회지
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• 제51권spc1호
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• pp.269-273
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• 2006

The study of molecular markers to improve crops largely depends on the availability of rapid and of efficient DNA extraction methods. Here we developed a cheap and convenient method to isolate genomic DNA from rice grains suitable for large-scale microsatellite analysis. We confirmed that the isolated rice DNA is suitable for PCR analysis with STS marker and SNP marker, as well as microsatellite marker. Further, we established high-throughput DNA extraction system in a 96-well plate format which make it possible high-throughput analysis of microsatellite markers with rice grains. This implies that the new method could be a useful tool for other types of marker analysis in large scale.

• 한국환경성돌연변이발암원학회지
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• 제15권2호
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• pp.100-105
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• 1995

The effects of DNA polymerase $\beta$ on the somatic chromosome mutations and mitotic recombinations were investigated using the transgenic Drosophila beating chimetic gene consisting of a promoter region of Drosophila actin 5C gene and rat DNA polymerase $\beta$. For detecting the somatic chromosome mutations and mitotic recombinations, the heterozygous (mwh/+) strains possessing or lacking transgene poi 13 were used. The spontaneous frequency of small mwh spots, due to deletion or nondisjunction etc., in the non-transgenic w strain and the transgenic p[pol $\beta$]-130 strain was 0.351 and 0.606, respectively. The spontaneous frequency (0.063) of large mwh spots, arises mostly from somatic recombination between the centromere and the locus mwh, in the transgenic p[pol $\beta$]-130 strain was about three times higher than that (0.021) of the non-transgenic w strain. The mutant clone frequencies of small and large mwh spots induced by N-methyl-N'-nitro-N-nitrosoguanidine and ethyl methanesulfonate in the transformant p[pol $\beta$]-130 were higher than those in the host strain w. The present results suggest that rat DNA polymerase $\beta$ participate at least in the somatic chromosome mutations and mitotic recombination processes.

• 한국미생물·생명공학회지
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• 제38권1호
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• pp.70-76
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• 2010

The single-stranded large circular (LC)-sense DNA were utilized as probes for DNA chip experiments. The microarray experiment using LC-sense DNA probes found differentially expressed genes in A549 cells as compared to WI38VA13 cells, and microarray data were well-correlated with data acquired from quantitative real-time RT-PCR. A 5K LC-sense DNA microarray was prepared, and the repeated experiments and dye swap test showed consistent expression patterns. Subsequent functional analysis using LC-antisense library of overexpressed genes identified several genes involved in A549 cell growth. These experiments demonstrated proper feature of LC-sense molecules as probe DNA for microarray and the potential utility of the combination of LC-sense microarray and antisense libraries for an effective functional validation of genes.

• Journal of Microbiology
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• 제44권1호
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• pp.29-34
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• 2006

The purpose of this study was to develop molecular identification method for medical mushrooms and their preparations based on the nucleotide sequences of nuclear large subunit (LSD) rDNA. Four specimens were collected of each of the three representative medicinal mushrooms used in Korea: Ganoderma Incidum, Coriolus versicolor, and Fomes fomentarius. Fungal material used in these experiments included two different mycelial cultures and two different fruiting bodies from wild or cultivated mushrooms. The genomic DNA of mushrooms were extracted and 3 nuclear LSU rDNA fragments were amplified: set 1 for the 1.1-kb DNA fragment in the upstream region, set 2 for the 1.2-kb fragment in the middle, and set 3 for the 1.3-kb fragment downstream. The amplified gene products of nuclear large subunit rDNA from 3 different mushrooms were cloned into E. coli vector and subjected to nucleotide sequence determination. The sequence thus determined revealed that the gene sequences of the same medicinal mushroom species were more than $99.48\%$ homologous, and the consensus sequences of 3 different medicinal mushrooms were more than $97.80\%$ homologous. Restriction analysis revealed no useful restriction sites for 6-bp recognition enzymes for distinguishing the 3 sequences from one another, but some distinctive restriction patterns were recognized by the 4-bp recognition enzymes AccII and HhaI. This analysis was also confirmed by PCR-RFLP experiments on medicinal mushrooms.

• Biotechnology and Bioprocess Engineering:BBE
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• 제7권3호
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• pp.121-129
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• 2002

Existing methods for optimization of sequences by random mutagenesis generate libraries with a small number of mostly deleterious mutations, resulting in libraries containing a large fraction of non-functional clones that explore only a small part of sequence space. Large numbers of clones need to be screened to find the rare mutants with improvements. Library display formats are useful to screen very large libraries but impose screening limitations that limit the value of this approach for most commercial applications. By contrast, in both classical breeding and in DNA shuffling, natural diversity is permutated by homologous recombination, generating libraries of very high quality, from which improved clones can be identified with a small number of complex screens. Given that this small number of screens can be performed under the conditions of actual use of the product, commercially relevant improvements can be reliably obtained.

• 미생물학회지
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• 제14권3호
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• pp.135-145
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• 1976

Confluent AGMK cells were infected by large plaque SV40 virus. Levels of DNA polymeras $({\alpha}\;and\;{\beta})$ were measured in the cytoplasm and the cell nucleus. The activities of DNA $polymerase-{\alpha}$ which found in both the cell nucleus and the cytoplasm were increased approximately eight folds at 48 hours after infection of SV40 virus. Only insignificant but constant amounts of DNA $polymerase-{\beta}$ were found either in the nucleus of the SV40 infected cell or of the uninfected cell. The characteristics of the SV40 virus induced DNA polymerases were compared with that of the uninfected cellular DNA polymerase in regard of the effects of pH, salt concentration, NEM concentration and temperature on those enzyme activities. No differential effect was found between both enzymes. Endouclease activities wre examined in the purified DNA $polymerase-{\alpha}\;and\;{\beta}$. The low level of endonuclease activity which might cut SV40 DNA 1 at one site was observed in the DNA $polymerase-{\alpha}$ whereas high but nonspecific endonuclease activities were found in the DNA $polymerase-{\beta}$.

• 농업과학연구
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• 제41권3호
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• pp.245-249
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• 2014

Among dozens of DNA polymerases cloned from thermophilic bacteria, Taq DNA polymerase from Thermus aquaticus has been most frequently used in polymerase chain reaction (PCR) that is being applied to gene cloning, DNA sequencing, gene expression analysis, and detection of infectious and genetic diseases. Since native Taq DNA polymerase is expressed at low level in T. aquaticus, recombinant Escherichia coli system was used to produce Taq DNA polymerase in a large amount. Taq DNA polymerase was expressed as a soluble form under the control of tac promoter in E. coli, and purified by heat treatment and ion exchange chromatographies. The purified Taq DNA polymerase was nearly homogeneous and exhibited a similar DNA amplification activity with a commercial Taq DNA polymerase.

• Genomics & Informatics
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• 제10권1호
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• pp.51-57
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• 2012

Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.

• Asian-Australasian Journal of Animal Sciences
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• 제21권1호
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• pp.11-18
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• 2008

We created a cDNA microarray representing approximately 3,500 pig genes for functional genomic studies. The array elements were selected from 6,494 cDNA clones identified in a large-scale expressed sequence tag (EST) project. These cDNA clones came from normalized and subtracted porcine adipose tissue cDNA libraries. Sequence similarity searches of the 3,426 ESTs represented on the array using BLASTN identified 2,790 (81.4%) as putative human orthologs, with the remainder consisting of "novel" genes or highly divergent orthologs. We used the gene microarray to profile transcripts expressed by adipose tissue of fatty Chinese Xiang pig (XP) and muscley Large White (LW). Microarray analysis of RNA extracted from adipose tissue of fatty XP and muscley LW identified 81 genes that were differently expressed two fold or more. Transcriptional differences of four of these genes, adipocyte fatty acid binding protein (aP2), stearyl-CoA desaturase (SCD), sterol regulatory element binding transcription factor 1 (SREBF1) and lipoprotein lipase (LPL) were confirmed using SYBR Green quantitative RT-PCR technology. Our results showed that high expression of SCD and SREBF1 may be one of the reasons that larger fat deposits are observed in the XP. In addition, our findings also illustrate the potential power of microarrays for understanding the molecular mechanisms of porcine development, disease resistance, nutrition, fertility and production traits.

• 대한의생명과학회지
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• 제10권2호
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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.