• The Korean Journal of Applied Statistics
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• v.23 no.6
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• pp.1067-1080
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• 2010

A number of methods have been developed to determine sample sizes in clinical trial, and most clinical trial organizations determine sample sizes based on the methods. In contrast, determining sufficient sample sizes needed for experiments using microarray chips is unsatisfactory and not widely in use. In this paper, our objective is to provide a guideline in determining sample sizes, utilizing reproducibility of real microarray data. In the reproducibility comparison, five methods for discovering differential expression are used: Fold change, Two-sample t-test, Wilcoxon rank-sum test, SAM, and LPE. In order to standardize gene expression values, both MAS5 and RMA methods are considered. According to the number of repetitions, the upper 20 and 100 gene accordances are also compared. In determining sample sizes, more realistic information can be added to the existing method because of our proposed approach.

• Archives of Plastic Surgery
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• v.37 no.4
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• pp.317-322
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• 2010

Purpose: There is no clear evidence of the original cause of hypertrophic scar, and the effective method of treatment is not yet established. Recently the steps of searching in gene and molecular level are proceeding. we are trying to recognize the difference between keratinocytes of hypertrophic scar and normal skin. Then we do support the comprehension of the scar formation mechanism and scar management. Methods: Total RNAs were extracted from cultured keratinocytes from 4 hypertrophic scars and normal skins. The cDNA chips were prepared. A total of 3063 cDNAs from human cDNA library were arrayed. And the scanning data were analyzed. Results: On microarray, heat shock protein, pyruvate kinase, tumor rejection antigen were more than 2 fold intensity genes. Among them, heat shock 70 kd protein showed the strongest intensity difference. Conclusion: In this study, it can be concluded that heat shock proteins play an important role in the process of wound healing and scar formation. This study provides basic biologic information for scar research. The new way of the prevention and treatment of scar formation would be introduced with further investigations.

• Journal of Information Processing Systems
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• v.2 no.3 s.4
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• pp.189-193
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• 2006

In this study we propose an automatic reading system for diagnostic DNA chips. We define a general specification for an automatic reading system and propose a possible implementation method. The proposed system performs the whole reading process automatically without any user intervention, covering image acquisition, image analysis, and report generation. We applied the system for the automatic report generation of a commercialized DNA chip for cervical cancer detection. The fluorescence image of the hybridization result was acquired with a $GenePix^{TM}$ scanner using its library running in HTML pages. The processing of the acquired image and the report generation were executed by a component object module programmed with Microsoft Visual C++ 6.0. To generate the report document, we made an HWP 2002 document template with marker strings that were supposed to be searched and replaced with the corresponding information such as patient information and diagnosis results. The proposed system generates the report document by reading the template and changing the marker strings with the resultant contents. The system is expected to facilitate the usage of a diagnostic DNA chip for mass screening by the automation of a conventional manual reading process, shortening its processing time, and quantifying the reading criteria.

• The Transactions of the Korean Institute of Electrical Engineers C
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• v.51 no.7
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• pp.328-334
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• 2002

The DNA chips are devices associating the specific recognition properties of two DNA single strands through hybridization process with the performances of the microtechnology. In the literature, the "Gene chip" or "DNA chip" terminology is employed in a wide way and includes macroarrays and microarrays. Standard definitions are not yet clearly exposed. Generally, the difference between macro and microarray concerns the number of active areas and their size, Macroarrays correspond to devices containing some tens spots of 500$\mu$m or larger in diameter. microarrays concern devices containing thousnads spots of size less than 500$\mu$m. The key technical parameters for evaluating microarray-manufacturing technologies include microarray density and design, biochemical composition and versatility, repreducibility, throughput, quality, cost and ease of prototyping. Here we report, a new method in which minute particles are arranged in a random fashion on a chip pattern using random fluidic self-assembly (RFSA) method by hydrophobic interaction. We intend to improve the stability of the particles at the time of arrangement by establishing a wall on the chip pattern, besides distinction of an individual particle is enabled by giving a tag structure. This study demonstrates the fabrication of a chip pattern, immobilization of DNA to the particles and arrangement of the minute particle groups on the chip pattern by hydrophobic interaction.ophobic interaction.

• The Journal of Korean Academy of Prosthodontics
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• v.55 no.4
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• pp.361-371
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• 2017

Purpose: We aimed to investigate the gene expression of human gingival fibroblasts on microgroove surface using DNA microarray. Materials and methods: Microgrooves were applied on grade II titanium discs to have 0/$0{\mu}m$ (NE0, control group), 60/$10{\mu}m$ (E60/10, experimental group) of respective width/depth by photolithography. The entire surface of the microgrooved Ti substrata was further acid etched and used as the two experimental groups in this study. Human gingival fibroblasts were cultured in the experimental group and the control group, and total RNA was extracted. The oligonucleotide microarray was performed to confirm the changes of various gene expression levels between experimental group and control group. Changes of gene expression level were determined at the pathway level by mapping the expression results of DNA chips, using the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis. Results: Gene expression levels on E60/10 and NE0 were analyzed, there were 123 genes showing significant differences in expression more than 1.5 times on E60/10 microgrooved surface compared to NE0 surface, and 19 genes showing significant differences in expression more than 2 times. The KEGG pathway analysis confirmed the changes in gene expression levels under experimental conditions. Cell signaling, proliferation, and activity among the various gene expression results were identified. Conclusion: Microgrooved surfaces induce gene expression changes and related cell signaling. According to the results of this study, microgrooves can be used as the surface of various biomaterials which need to improve cell activity through gene expression changes and activation of cell signaling.

• Korean Journal of Food Science and Technology
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• v.35 no.4
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• pp.591-597
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• 2003

To compare the quality of genomic DNA extracted from potato for PCR detection, four different methods, such as silica-based membrane method, silica-coated bead method, STE solution treatment, and CTAB-phenol/chloroform method, were evaluated. Also, to remove an excessive carbohydrate from the potato, ${\alpha}$- and ${\beta}$-amylase were used individually and in combination. When used both silica-based membrane method and silica-coated bead method combined with enzymes, the genomic DNAs were extracted from the raw potato with high purity for PCR. However, the silica-coated head method combined with enzyme treatment was the most efficient for extraction of the genomic DNA from the frozen fried potatoes. When applied with STE solution, the highly purified DNA was extracted from the raw potatoes without enzyme treatment in adequate yield for PCR. In cases of processed potatoes, such as frozen-fried potato and fabricated potato chips, CTAB-phenol/chloroform method is mostly feasible for DNA extraction and PCR efficacy at high sensitivity. As the results of PCR amplification, 216bp of PCR product was detected on 2% agarose gel electrophoresis, but any amplicons derived from New leaf and New leaf Y gene was not detected in any sample.

• International Journal of Oral Biology
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• v.37 no.4
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• pp.181-188
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• 2012

As the demand for large-scale analysis of gene expression using DNA arrays increases, the importance of the surface characterization of DNA arrays has emerged. We compared the efficiency of molecular biological applications on solid-phases with different surface polarities to identify the most optimal conditions. We employed thiol-gold reactions for DNA immobilization on solid surfaces. The surface polarity was controlled by creating a self-assembled monolayer (SAM) of mercaptohexanol or hepthanethiol, which create hydrophilic or hydrophobic surface properties, respectively. A hydrophilic environment was found to be much more favorable to solid-phase molecular biological manipulations. A SAM of mercaptoethanol had the highest affinity to DNA molecules in our experimetns and it showed greater efficiency in terms of DNA hybridization and polymerization. The optimal DNA concentration for immobilization was found to be 0.5 ${\mu}M$. The optimal reaction time for both thiolated DNA and matrix molecules was 10 min and for the polymerase reaction time was 150 min. Under these optimized conditions, molecular biology techniques including DNA hybridization, ligation, polymerization, PCR and multiplex PCR were shown to be feasible in solid-state conditions. We demonstrated from our present analysis the importance of surface polarity in solid-phase molecular biological applications. A hydrophilic SAM generated a far more favorable environment than hydrophobic SAM for solid-state molecular techniques. Our findings suggest that the conditions and methods identified here could be used for DNA-DNA hybridization applications such as DNA chips and for the further development of solid-phase genetic engineering applications that involve DNA-enzyme interactions.

• The Korean Journal of Mycology
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• v.44 no.4
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• pp.240-246
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• 2016

During a survey of the activities of fungi in steamed sweet potato, stored garlic, agricultural by-products for mushroom cultivation media, and pinewood chips from a pinewood nematode-infected tree, numerous fungal samples were isolated and identified. This study identified five species that have not been previously reported in Korea, namely Geomyces pannorum, Neopestalotiopsis javaensis, Penicillium allii, Penicillium chermesinum, and Ophiognomonia setacea. For all identified species, the cultural features of colonies formed on growth media, their morphological characteristics observed by a light microscope, and their molecular phylogenetic relationships based on nucleotide sequences of the internal transcribed spacer rDNA region or calmodulin gene were described.

• Journal of Animal Science and Technology
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• v.65 no.1
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• pp.57-68
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• 2023

Flavor is an important sensory trait of chicken meat. The free amino acid (FAA) and nucleotide (NT) components of meat are major factors affecting meat flavor during the cooking process. As a genetic approach to improve meat flavor, we performed a genome-wide association study (GWAS) to identify the potential candidate genes related to the FAA and NT components of chicken breast meat. Measurements of FAA and NT components were recorded at the age of 10 weeks from 764 and 767 birds, respectively, using a White leghorn and Yeonsan ogye crossbred F2 chicken population. For genotyping, we used 60K Illumina single-nucleotide polymorphism (SNP) chips. We found a total of nine significant SNPs for five FAA traits (arginine, glycine, lysine, threonine content, and the essential FAAs and one NT trait (inosine content), and six significant genomic regions were identified, including three regions shared among the essential FAAs, arginine, and inosine content traits. A list of potential candidate genes in significant genomic regions was detected, including the KCNRG, KCNIP4, HOXA3, THSD7B, and MMUT genes. The essential FAAs had significant gene regions the same as arginine. The genes related to arginine content were involved in nitric oxide metabolism, while the inosine content was possibly affected by insulin activity. Moreover, the threonine content could be related to methylmalonyl-CoA mutase. The genes and SNPs identified in this study might be useful markers in chicken selection and breeding for chicken meat flavor.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.3
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• pp.327-334
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• 2018

Objective: The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. Methods: Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ${\geq}90%$ and minor allele frequency (MAF) ${\geq}0.01$, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at $3.28{\times}10^{-6}$ (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. Results: By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds. Conclusion: This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study.