• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.739-740
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• 2001

DNA microarray with a set of 37 Corynebacterium glutamicum genes encoding enzymes for primary metabolism of glycolysis, TCA cycle and lysine biosynthesis, anaplerosis etc was constructed on slide glass in triplicate. With this DNA microarray, metabolic characteristics of the lysine-producing strain was analyzed during different phase of the cultivation. The major differences in using glucose as a carbon source instead of sucrose was found in the anaplerolytic enzymes, which control the interconversion of C3 and C4 metabolites. Also, the expression profile of these major enzymes was found to be quite distinct among different phases of growth.

• Fisheries and Aquatic Sciences
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• v.6 no.2
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• pp.101-104
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• 2003

A cDNA clone for the olive flounder (Paralichthys olivaceus) transferrin receptor (fTfR) was isolated from a leukocytes cDNA library. The fTfR gene consisted of 2,319 bp encoding 773 amino acid residues. The amino acid sequence alignment of the fTfR showed that their size and hydrophobic profile are similar. In addition, the Tyr-Thr-Arg-Phe (YTRF) motif that is the recognition signal for high-efficiency endocytosis, is conserved very well. This motif is important for functional properties of TfR. The deduced amino acid sequence had $42.4-42.9\%$ identities with the previously reported TfRs of vertebrates. The fTfR was expressed in the blood, kidney, spleen, and liver of healthy olive flounder by the Northern blot hybridization.

• Journal of Integrative Natural Science
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• v.5 no.3
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• pp.163-167
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• 2012

UV spectrophotometer was used to detect protein-DNA complex from DNA melting profile under constant temperature increase. Melting temperature (Tm) was $43^{\circ}C$ in copA duplex DNA alone. In the presence of Proteus mirabilis transcription regulator protein (PMTR) protein at 0.2 and 0.4 ${\mu}M$, Tm's were $45{\pm}0.5$ and $47.6{\pm}0.6^{\circ}C$, respectively. According to fluorescence polarization and gel shift assay. PMTR:copA complex was detected by the retarded migration on gel and the dissociation constant ($K_d$) was $(9.2{\pm}2.8){\times}10^{-9}M$.

• Journal of Korean Society of Forest Science
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• v.95 no.4
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• pp.388-392
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• 2006

To investigate physiological characteristics and genetic diversity of Rhizina undulata isolates distributed in Korea, cultural characteristics and random amplified polymorphic DNA (RAPD) of 13 Rhizina undulata isolates from Pinus densiflora and P. thunbergi stands were analyzed. There were no correlations between the host species of R. undulata isolates and the mycelial growth of R. undulata isolates on culture media supplemented with water-soluble extract from the two different host species, i.e., Pinus densiflora and P. thunbergi. Genetic diversity of genomic DNA from 13 R. undulata isolates was analyzed by RAPD using 12 random primers. There was no differentiation in RAPD profiles among the isolates from Korea. But, there was some differentiation in RAPD profiles between Korean isolates and Japanese isolates, with 88% homology by phylogenetic tree analysis.

• Horticultural Science & Technology
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• v.35 no.1
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• pp.98-107
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• 2017

A DNA profile database was constructed to investigate the genetic relatedness of 72 germplasm samples of Pyrus and related cultivars using microsatellite markers. Three P. pyrifolia, four P. commus, and one P. betulifolia cultivars with different morphological traits were screened using 387 pairs of microsatellite primers. A core set of 11 primer pairs was selected to obtain 133 polymorphic amplified fragments meeting three criteria: high polymorphism information contents (PIC), high repeatability, and distinct allele patterns. The number of alleles per locus ranged between 4 and 22. Average PIC was 0.743 (range: 0.557 - 0.879). Cluster analysis using the unweighted pair - group method with arithmetical average (UPGMA) separated the 72 pear cultivars and germplasm samples into four major groups: Chinese, European pears, and a cluster of 55 Asian pears that could be reclassify into two subcluster, I - $1^{st}$ and II - $2^{nd}$, according to pedigree information. Almost all of the cultivars were discriminated by 11 microsatellite marker genotypes. The microsatellite DNA profile database may be utilized as tool to verify distinctness, uniformity, and stability between candidate cultivar, and to verify in the distinctness of existing cultivars.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.1
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• pp.3-12
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• 2018

Objective: DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods: A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates). The reference pig genome was annotated with 78.5% of the raw reads. A total of 33,506 putative methylated regions (PMR) were identified from methylated regions that overlapped at least two samples. Results: Of these, only 3.1% were commonly observed in all eight samples. DNA methylation patterns between two littermates were as diverse as between unrelated individuals (p = 0.47), indicating that maternal genetic effects have little influence on the variation in DNA methylation of porcine LDM. The highest density of PMR was observed on chromosome 10. A major proportion (47.7%) of PMR was present in the repeat regions, followed by introns (21.5%). The highest conservation of PMR was found in CpG islands (12.1%). These results show an important role for DNA methylation in species- and tissue-specific regulation of gene expression. PMR were also significantly related to muscular cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism. Conclusion: This study indicated the biased distribution and functional role of DNA methylation in gene expression of porcine LDM. DNA methylation was related to cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism (e.g., insulin signaling pathways). Nutritional and environmental management may have a significant impact on the variation in DNA methylation of porcine LDM.

• Molecular & Cellular Toxicology
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• v.5 no.1
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• pp.51-57
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• 2009

Quantum Dot (QD) nanoparticles are used in various industrial applications, such as diagnostic, drug delivery, and imaging agents of biomedicine. Although QDs are extensively used in many medical science, several studies have been demonstrated the potential toxicity of nanoparticles. The first objective of this study was to investigate the nanotoxicity of QDs in the HaCaT human keratinocyte cell line by focusing on gene expression pattern. In order to evaluate the effect of QDs on gene expression profile in HaCaT cells, we analyzed the differential genes which related to oxidative stress and antioxidant defense mechanisms by using human cDNA microarray and PCR array. A human cDNA microarray was clone set, which was sorted for a list of genes correlated with cell mechanisms. We tried to confirm results of cDNA microarray by using PCR array, which is pathway-focused gene expression profiling technology using Real-Time PCR. Although we could not find the exactly same genes in both methods, we have screened the effects of QDs on global gene expression profiles in human skin cells. In addition, our results show that QD treatment somehow regulates cellular pathways of oxidative stress and antioxidant defense mechanisms. Therefore, we suggest that this study can enlarge our knowledge of the transcriptional profile and identify new candidate biomarker genes to evaluate the toxicity of nanotoxicology.

• Parasites, Hosts and Diseases
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• v.56 no.3
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• pp.229-236
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• 2018

Cutaneous leishmaniasis (CL) has been one of the most common parasitic diseases in Saudi Arabia. This study exhibits the clinical features, diagnosis, cytokine profile and treatment of CL patients in Al-Taif province. Ninety CL suspects at a tertiary care general hospital were enrolled in one-year study. Patients were interviewed, clinically-examined, and subjected to laboratory tests: skin scraping smear microscopy, OligoC-TesT commercial PCR (Coris BioConcept) and kinetoplast DNA (kDNA) PCR for Leishmania diagnosis. Interferon-gamma (RayBio; Human $IFN-{\gamma}$ ) and nitric oxide (NO) levels in patients' sera were evaluated before treatment with sodium stibogluconate (pentostam) with 20-day intramuscular drug regimen. Positive rates of microscopy, commercial PCR and kDNA PCR were 74.4%, 95.5% and 100%, respectively. Patients came to hospital mostly in winter (45.0%). CL was frequently exhibited in Saudi patients (78.8%), male gender (70.7%), age <20 years (50.0%), rural-dwellers (75.5%) and patients with travel history (86.6%). Lesion was mostly single ulcer (93.3%), occurred in the face (67.7%). Upon pentostam treatment, 85.1% of ulcers showed rapid healing signs. Levels of $IFN-{\gamma}$ and NO were significantly higher in the healing than the non-healing cases (P<0.001). The kDNA PCR proved more sensitive than microscopy and OligoC-TesT commercial PCR. Our results open perspectives for $IFN-{\gamma}$ use as a biomarker predicting treatment response.

• Proceedings of the Korean Society of Toxicology Conference
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• 2000.11a
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• pp.31-41
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• 2000

The major issue in the post genome sequencing era is determination of gene expression patterns in variety of biological systems. A microarray system is a powerful technology for analyzing the expression profile of thousands of genes at one experiment. In this study, we constructed cDNA microarray which carries 2,304 cDNAS derived from oligo-capped mouse cDNA library. Using this hand-made microarray we determined gene expression in various biological systems. To determine tissue specific genes, we compared Nine genes were highly-expressed in adult mouse brain compared to kidney, liver, and skeletal muscle. Tissue distribution analysis using DNA microarray extracted 9 genes that were predominantly expressed in the brain. A database search showed that five of the 9 genes, MBP, SC1, HiAT3, S100 protein-beta, and SNAP25, were previously known to be expressed at high level in the brain and in the nervous system. One gene was highly sequence similar to rat S-Rex-s/human NSP-C, suggesting that the gene is a mouse homologue. The remaining three genes did not match to known genes in the GenBank/EMBL database, indicating that these are novel genes highly-expressed in the brain. Our DNA microarray was also used to detect differentiation specific genes, hormone dependent genes, and transcription-factor-induced genes. We conclude that DNA microarray is an excellent tool for identifying differentially expressed genes.

• KSBB Journal
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• v.16 no.6
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• pp.538-546
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• 2001

An integrated data analysis program for DNA chip containing normalization, FDM analysis, various kinds of clustering methods, PCA, and SVD was applied to analyze combined yeast cell cycle data. This paper includes both comparisons of some clustering algorithms such as K-means, SOM and furry c-means and their results. For further analysis, clustering results from the integrated analysis program was used for function assignments to each cluster and for motif analysis. These results show an integrated analysis view on DNA chip data.