• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.22-26
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• 2002

There are a number of ways in which environmental microbiology and microbial ecology will benefit from DNA micro array technology. These include community genome arrays, SSU rDNA arrays, environmental functional gene arrays, population biology arrays, and there are clearly more different applications of microarray technology that can be applied to relevant problems in environmental microbiology. Two types of the applications, bacterial identification chip and functional gene detection chip, will be presented. For the bacterial identification chip, a new approach employing random genome fragments that eliminates the disadvantages of traditional DNA-DNA hybridization is proposed to identify and type bacteria based on genomic DNA-DNA similarity. Bacterial genomes are fragmented randomly, and representative fragments are spotted on a glass slide and then hybridized to test genomes. Resulting hybridization profiles are used in statistical procedures to identify test strains. Second, the direct binding version of microarray with a different array design and hybridization scheme is proposed to quantify target genes in environmental samples. Reference DNA was employed to normalize variations in spot size and hybridization. The approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal ratio.

• Proceedings of the Korean Information Science Society Conference
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• 2005.11b
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• pp.289-291
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• 2005

최근 유전자 칩의 발전으로 다양하고 방대한 양의 유전자 정보를 이용한 정확하고 신뢰성 높은 분류, 군집 및 질병을 예측하는 분석 기법이 증가하고 있다. 하지만 특징적인 유전자를 선택하는 Gene Selection 기법의 종류는 많지가 않으며 주로 통계적인 방법에 의존하여 유전자를 선택하는 기법을 많이 사용하고 있다. 본 논문에서는 유전자 알고리즘과 신경망의 결합을 통한 데이터마이닝을 기반으로 신뢰성 높은 특징적인 유전자를 선택하는 Gene Selection 기법에 대하여 연구을 진행하였다.

• Proceedings of the KIEE Conference
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• 2006.07c
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• pp.1322-1323
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• 2006

This research aims to develop the multiple channel electrochemical DNA chip that has the above characteristic and be able to solve the problems. At first, we fabricated a high integration type DNA chip array by lithography technology. It is able to detect a plural genes electrochemically after immobilization of a plural probe DNA and hybridization of non-labeling target DNA on the electrodes simultaneously.

• Plant Biotechnology Reports
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• v.2 no.4
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• pp.233-238
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• 2008

Kadainou R-1, an interspecific hybrid grape derived from red (Vitis ficifolia var. ganebu) and white (V. vinifera cv. Muscat of Alexandria) grapes, accumulates high concentrations of anthocyanin in the berry skin. Hence, the expression of uridine 50 -diphosphate (UDP)-glucose:flavonoid 3-O-glucosyltransferase (UFGT), the key enzyme of the anthocyanin pathway, was examined in the berry skin of Kadainou R-1. As information on gene sequences of V. ficifolia var. ganebu and other wild grape species was unavailable, we performed GeneChip hybridization using biotin-labeled genomic deoxyribonucleic acid (DNA) to investigate how the genomic sequences of V. vinifera varieties and that of V. ficifolia var. ganebu differ. The study showed a lower correlation coefficient between V. vinifera cultivars and V. ficifolia var. ganebu than that among V. vinifera cultivars. The sequences of the UFGT gene derived from both parents of the red and white cultivars were sequenced in Kadainou R1 and revealed that both were expressed irrespective of the fact that it was not expressed in the white grape (male parent).

• Genomics & Informatics
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• v.9 no.2
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• pp.89-91
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• 2011

DNA chips are becoming increasingly popular as a convenient way to perform vast amounts of experiments related to genes on a single chip. And the importance of analyzing the data that is provided by such DNA chips is becoming significant. A very important analysis on DNA chip data would be clustering genes to identify gene groups which have similar properties such as cancer. Clustering data for DNA chips usually deal with a large search space and has a very fuzzy characteristic. The Particle Swarm Optimization algorithm which was recently proposed is a very good candidate to solve such problems. In this paper, we propose a clustering mechanism that is based on the Particle Swarm Optimization algorithm. Our experiments show that the PSO-based clustering algorithm developed is efficient in terms of execution time for clustering DNA chip data, and thus be used to extract valuable information such as cancer related genes from DNA chip data with high cluster accuracy and in a timely manner.

• 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.

• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.119-122
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• 2000

Biological science is being revolutionized by the availability of much sequence information from many genome project With the advanced technology at hand, main trend in biological research is rapidly changing from a structural DNA analysis to understanding cellular function of the DNA sequences. Combined with mechanics, computer, bioinformatics and other advanced technologies, DNA chip technology provides numerous applications because of its robustness, accuracy, and automation. DNA chip is expected to become an indispensable tool in fields of biology, biotechnology, drug discovery, and other application areas. DNA chip can be used for mutation and polymorphism detection, gene expression monitoring and phenotypic analysis as well. If DNA chip is used for the development of pharmaceutical products, it can considerably reduce the cost and time for the entire process of drug discovery and development, and can also contribute in developing personal drugs.

• The Korea Genome Conference
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• 2005.09a
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• pp.94-94
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• 2005

• 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.

• Environmental Mutagens and Carcinogens
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• v.26 no.1
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• pp.1-6
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• 2006

To enhance our understanding of toxicity mediated through the pathway by which TCDD stimulates gene expression, we have investigated genes whose expressions are changed after treatment with TCDD and/or MNNG in human Chang liver cell. First, we treated with MNNG and TCDD for two weeks to transform human Chang liver cell. We obtained cell looks like to be transformed and compared the differential gene expression by using cDNA chip (Macrogen) which carrys genes related with signal transduction pathways, oncogenes and tumor suppressor genes, etc. We found that TCDD up- or down-regulated 203 and 111 genes including oncogenes and tumor suppressor genes in human Chang liver cell two fold or more, respectively. Second, we compared the differential gene expression after treatment with TCDD only by using cDNA chip (Superarray) which carrys genes related with cell cycle regulations, and found that TCDD up regulated genes related with cell proliferation as well as cell growth inhibition in human Chang liver cell two fold or more, respectively. These results suggest that toxicity induced by TCDD may reflect sustained alterations in the expression of many genes and that the changes reflect both direct and indirect effects of TCDD.