• Proceedings of the Optical Society of Korea Conference
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• 2005.07a
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• pp.306-307
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• 2005

• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.231-239
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• 2016

To study the transcript levels of epigenetically regulated genes in tobacco, we have developed a transgenic line OX1 overexpressing NtROS2a gene encoding cytosine DNA demethylation and a RNAi plant line RNAi13. It has been reported that salt- and $H_2O_2$-stress tolerance of these transgenic lines are enhanced with various phenotypic characters (Lee et al. 2015). In this paper, we conducted microarray analysis with Agilent Tobacco 4 x 44K oligo chip by using overexpression line OX1, RNAi plant line RNAi 13, and wild type plant WT. Differentially expressed genes (DEGs) related to metabolism, nutrient supply, and various stressed were up-regulated by approximately 1.5- to 80- fold. DEGs related to co-enzymes, metabolism, and methylation functional genes were down-regulated by approximately 0.03- to 0.7- fold. qRT-PCR analysis showed that the transcript levels of several candidate genes in OX1 and RNAi lines were significantly (p < 0.05) higher than those in WT, such as genes encoding KH domain-containing protein, MADS-box protein, and Zinc phosphodiesterase ELAC protein. On the other hand, several genes such as those encoding pentatricopeptide (PPR) repeat-containing protein, histone deacetylase HDAC3 protein, and protein kinase were decreased by approximately 0.4- to 1.0- fold. This study showed that NtROS2a gene encoding DNA glycosylase related to demethylation could regulate adaptive response of tobacco at transcriptional level.

• KSBB Journal
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• v.20 no.3
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• pp.220-227
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• 2005

Doxorubicin is an anthracycline-family polyketide compound with a very potent anti-cancer activity, typically produced by Streptomyces peucetius. To understand the potential target biosynthetic genes critical for the doxorubicin everproduction, a doxorubicin-specific DNA microarray chip was fabricated and applied to reveal the growth-phase-dependent expression profiles of biosynthetic genes from two doxorubicin-overproducing strains along with the wild-type strain. Two doxorubicin-overproducing 5. peucetius strains were generated via over-expression of a dnrl (a doxorubicin-specific positive regulatory gene) and a doxA (a gene involved in the conversion from daunorubicin to doxorubicin) using a streptomycetes high expression vector containing a strong ermE promoter. Each doxorubicin-overproducing strain was quantitatively compared with the wild-type doxorubicin producer based on the growth-phase-dependent doxorubicin productivity as well as doxorubicin biosynthetic gene expression profiles. The doxorubicin-specific DNA microarray chip data revealed the early-and-steady expressions of the doxorubicin-specific regulatory gene (dnrl), the doxorubicin resistance genes (drrA, drrB, drrC), and the doxorubicin deoxysugar biosynthetic gene (dnmL) are critical for the doxorubicin overproduction in S. peucetius. These results provide that the relationship between the growth-phase-dependent doxorubicin productivity and the doxorubicin biosynthetic gene expression profiles should lead us a rational design of molecular genetic strain improvement strategy.

• Genomics & Informatics
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• v.1 no.2
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• pp.94-100
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• 2003

Motivation: Many have observed a nonlinear relationship between the signal intensity and the transcript abundance in microarray data. The first step in analyzing the data is to normalize it properly, and this should include a correction for the nonlinearity. The commonly used linear normalization schemes do not address this problem. Results: Nonlinearity is present in both cDNA and oligonucleotide arrays, but we concentrate on the latter in this paper. Across a set of chips, we identify those genes whose within-chip ranks are relatively constant compared to other genes of similar intensity. For each gene, we compute the sum of the squares of the differences in its within-chip ranks between every pair of chips as our statistic and we select a small fraction of the genes with the minimal changes in ranks at each intensity level. These genes are most likely to be non-differentially expressed and are subsequently used in the normalization procedure. This method is a generalization of the rank-invariant normalization (Li and Wong, 2001), using all available chips rather than two at a time to gather more information, while using the chip that is least likely to be affected by nonlinear effects as the reference chip. The assumption in our method is that there are at least a small number of non­differentially expressed genes across the intensity range. The normalized expression values can be substantially different from the unnormalized values and may result in altered down-stream analysis.

• Maxillofacial Plastic and Reconstructive Surgery
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• v.35 no.4
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• pp.227-235
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• 2013

Purpose: High risk human papillomavirus (HPV) is the main source of cervical cancer, nearly up to 100%. Because there are no affordable data regarding the incidence of HPV in different sites of oral cavity, the purpose of this study is to review the previous article and to find out about the incidence and types of HPV in specific areas of oral cavity. Methods: We examined a total of 106 patients with oral cavity cancer for HPV detection. Available DNA chip (MY-HPV chip kit$^{(R)}$, Mygene Co., Korea) was used for the detection of low risk HPV types (6, 11, 34, 40, 42, 43, 44) and high risk HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 54, 56, 58). Patients were previously diagnosed as invasive cancer of oral cavity. Specimen used for HPV detection was extracted from the main mass during resection and were tested for HPV type, performed by a DNA chip method. Results: Histologic results showed that there were squamous cell carcinomas, mucoepidermoid carcinomas, cystadenocarcinomas, leiomyosarcoma and etc. Among HPV positive cancer, 2 patients showed positive for high risk HPV type 16, 3 patients showed positive for low risk HPV type 6 and the other 2 patients were positive for other types of HPV. Of the 7 patients with HPV positive, 4 patients were on the tongue, 3 on the lower gingiva. Conclusion: Most of the HPV positive cancers were on the tongue in our study. Cervical cancer of HPV infection is reported to be increasing in our society and because HPV infection largely spreads by sexual contact, the incidence of oral cancer with HPV infection is greatly assumed to be on the increase, simultaneously. Because the incidence of HPV on specific areas of oral cavity among oral cancer patients is not identified, more studies are ongoing.

• 제어로봇시스템학회:학술대회논문집
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• 2003.10a
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• pp.2226-2229
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• 2003

A new method is presented to construct a classifier. This was accomplished by combining a generalized regression neural network (GRNN) and a genetic algorithm (GA). The classifier constructed in this way is referred to as a GA-GRNN. The GA played a role of controlling training factors simultaneously. In GA optimization, neuron spreads were represented in a chromosome. The proposed optimization method was applied to a data set, consisted of 4 different promoter sequences. The training and test data were composed of 115 and 58 sequence patterns, respectively. The range of neuron spreads was experimentally varied from 0.4 to 1.4 with an increment of 0.1. The GA-GRNN was compared to a conventional GRNN. The classifier performance was investigated in terms of the classification sensitivity and prediction accuracy. The GA-GRNN significantly improved the total classification sensitivity compared to the conventional GRNN. Also, the GA-GRNN demonstrated an improvement of about 10.1% in the total prediction accuracy. As a result, the proposed GA-GRNN illustrated improved classification sensitivity and prediction accuracy over the conventional GRNN.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2005.10a
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• pp.334-338
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• 2005

식육의 소비형태가 변화함에 따라 생체 기능성물질의 탐색과 이용에 관한 연구가 활성화 되어지고 있다. 식품에 소량 존재하며 지방세포분화를 촉진하는 물질로 밝혀진 conjugated linoleic acid (CLA)중 9c-11c(9c)가 3원 교잡종 암퇘지(Yorkshire ${\times}$ Landrace ${\times}$ Duroc)의 어떤 유전자에 영향을 줌으로써 지방세포의 분화를 촉진하는지 DNA chip을 이용하여 분석하였다. 분석도구로는 Genepix 6.0과 Vector Xpression 3.0을 사용하였다. 분석결과 $Na^+,\;K^+$-ATPase, ciliary neurotrophic factor, complement cytolysis inhibitor, prolactin receptor, type II collagen alpha1 등 과 같은 분화 관련 유전자가 나타났다. 이 연구는 나아가 DNA chip을 이용해서 지방세포 분화억제에 관여하는 유전자를 찾아내고, 이 유전자들은 지방세포 분화 조절과 비만관련 연구에 활용될 것이다.

• The Journal of Advanced Prosthodontics
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• v.6 no.6
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• pp.555-558
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• 2014

Focal epithelial hyperplasia (FEH) is a human papillomavirus (HPV)-induced alteration of the oral mucosa that presents with a clinically distinct appearance. While other HPV-infected lesions such as squamous papilloma, verruca vulgaris, and condyloma acuminatum involve the skin, oral mucosa, and genital mucosa, FEH occurs only in the oral mucosa. The affected oral mucosa exhibits multiple papules and nodules with each papule/nodule being flat-topped or sessile. The affected region resembles the normal color of oral mucosa rather than appearing as a white color since the epithelial surface is not hyperkeratinized. Almost all cases present with multiple sites of occurrence. This rare, benign epithelial proliferation is related to low-risk HPV, especially HPV-13 and -32, and is not transformed into carcinoma. We report a case of FEH that arose on the attached gingiva of an East Asian male adult related to prosthesis without detection of any HPV subtype in HPV DNA chip and sequencing.

• BioChip Journal
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• v.12 no.4
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• pp.304-308
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• 2018

Atopic disease is caused by a complex combination of environmental factors and genetic factors, and studies on influence of exposure to various environmental factors on atopic diseases are continuously reported. However, the exact cause of atopic dermatitis is not yet known. Our study was conducted to analyse the association of SNPs with the development of atopic disease in a small cohort. Samples were collected from the Mothers' and Children's Environmental Health (MOCEH) study and 192 cord blood DNA samples were used to identify incidence of atopy due to influence of exposure to environmental factors. Genetic elements were analysed using a precision medicine research (PMR) array designed with various SNPs for personalized medicine. Case-control analysis of atopy disease revealed 253 significant variants (p<0.0001) and SNPs on five genes (CARD11, ZNF365, KIF3A, DMRTA1, and SFMBT1) were variants identified in previous atopic studies. These results are important to confirm the genetic mutation that may lead to the onset of foetal atopy due to maternal exposure to harmful environmental factors. Our results also suggest that a small-scale genome-wide association analysis is beneficial to confirm specific variants as direct factors in the development of atopy.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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• v.19 no.2
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• pp.77-87
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• 2006

Objectives : We studied Effect of Platycodon grandiflorum on Lung carcinoma Methods : By using cDNA microarray technique, we analyzed the effects of AEPG(aqueous extract of Platycodon grandiflorum) on the gene expression profile. Results : Out of 384 genes screened associated with growth inhibition of carcinoma cell, 9 genes were founded to be affected in their expression levels by more than 1.2-fold after treatment with AEPG. And 67 genes were changed the expression level 0.5 times more than that of reference RNA after treatment of AEPG. Conclusions: These findings suggest that P. grandiflorum has strong potential for development as an agent for prevention and treatment against human lung cancer.