• Journal of Life Science
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• v.25 no.4
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• pp.376-384
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• 2015

To investigate the molecular events of controlling intramuscular fat (or marbling), which is an important factor in the evaluation of beef quality, we performed cDNA microarray analyses using the longissimus dorsi muscle and back fat tissues. For this study, we constructed normalized cDNA libraries: fat tissues in native Korean cattle (displaying 1,211 specific genes), and muscle tissues in native Korean cattle (displaying 1,346 specific genes). A bovine cDNA chip was constructed with 1,680 specific genes, consisting of 760 genes from muscle tissues and 920 genes from fat tissues. The microarray analysis in this experiment showed a number of differentially expressed genes, which compared the longissimus dorsi muscle (Cy5) with back fat tissue (Cy3). Among many specific differentially expressed genes, 12-lipoxygenase (oxidizing esterified fatty acids) and prostaglandin D synthase (differentiation of fibroblasts to adipocytes) are the key candidate enzymes that should be involved in controlling the accumulation of intramuscular fat. In this study, differentially and commonly expressed genes in the muscle and fat tissues of native Korean cattle were found in large numbers, using the hybridization assay. The expression levels of the selected genes were confirmed by semi-quantitative RT-PCR, and the results were similar to those of the cDNA microarray.

• 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.

• Journal of the Korean Institute of Intelligent Systems
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• v.16 no.5
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• pp.556-561
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• 2006

It is very important to classify the DNA Chip image pattern in order to acquire useful information about genetic disease of people. In this paper, we developed the novel pattern classification method of DNA Chip image using MLP based back-propagation and Self organizing Map learning algorithm. And then we compared and analyzed these classified pattern results. Also we carried out experiment in the MV2440 board using CPU Cote for S3C2440(ARM 920T) and PC environment, and displayed its results in order to give the genetic information to user mote easily in various environment.

• The Transactions of the Korean Institute of Electrical Engineers C
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• v.51 no.2
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• pp.92-97
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• 2002

One of the important roles of a DNA chip is the capability of detecting genetic diseases and mutations by analyzing DNA sequence. For a successful electrochemical genotyping, several aspects should be considered including the chemical treatment of electrode surface, DNA immobilization on electrode, hybridization, choice of an intercalator to be selectively bound to double standee DNA, and an equipment for detecting and analyzing the output signal. Au was used as the electrode material, 2-mercaptoethanol was used for linking DNA to Au electrode, and methylene blue was used as an indicator that can be bound to a double stranded DNA selectively. From the analysis of reductive current of this indicator that was bound to a double stranded DNA on an electrode, a normal double stranded DNA was able to be distinguished from a single stranded DNA in just a few seconds. Also, it was found that the peak reduction current of indicator is proportional to the concentration of target DNA to be hybridized with probe DNA. Therefore, it is possible to realize a sim71e and cheats DNA sensor using the electrochemical measurement for genotyping.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 2003.10a
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• pp.173-173
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• 2003

With the introduction of DNA microarrays, a high throughput analysis of gene expression is now possible as a replacement to the traditional time-consuming Southern-blot analysis. This cDNA microarray should be ahighly favored technology in the area of molecular toxicology or analysis of environmental stresses.In this study, therefore, we developed a novel cDNA microarray for analyzing stress-specific responses in japanese Medaka fish. In the design and fabrication of this stress specific functional cDNA microarray, 123 different genes in Medaka fish were selected from eighteen different stress responsive groups and spotted on a 25${\times}$75 mm glass surface. After exposure of the fish to bisphenol A which is the one of the well-known endocrine disrupting chemicals (EDCs), over 1 or 10 days, the responses of the DNA chip were found to show distinct expression patterns according to the mode of toxic actions from environmental toxicants. As a results, they showed specific gene expression pattern to bisphenol A, additionally, the chemical spesific biomarkers could be suggested based on the chip analysis data. Therefore, this chip can be used to monitor stress responses of unknown and/or known toxic chemicals using Medaka fish and may be used for the further development of biomarkers by utilizing the gene expression patterns for known contaminants.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.28 no.8C
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• pp.803-810
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• 2003

This paper addresses an image processing technique for the human papillomavirus (HPV) DNA chip to discriminate whether the probes are hybridized with the target DNA. HPV DNA chip is designed to determine HPV gene-types by using DNA probes for 22 HPV types. In addition to the probes, the HPV DNA chip has markers that always react with the sample DNA. The positions of probe-dots in the final scanned image are fixed relative to the marker- dot locations with a small variation attributable to the accuracy of the dotter and the scanner. The probes are quadruplicated to enhance diagnostic fidelity. frier knowledge including the marker relative distance and the replication information of probes is integrated into the template matching technique with normalized covariance measure. It was demonstrated that the employment of both of the prior knowledges can be accomplished by simply averaging the template matching measures over the positions of the markers and probes. The resulting proposed scheme yields stable marker locating and probe classification.

• Fisheries and Aquatic Sciences
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• v.8 no.3
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• pp.122-127
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• 2005

A DNA chip that rapidly and accurately detects the viral genes in rhabdovirus-infected fish was developed. The N, Ml, and G proteins of three rhabdovirus strains, infectious hematopoietic necrosis virus (IHNV), viral hemorrhagic septicemia virus (VHSV), and flounder rhabdovirus (HIRRV), were selected for use as probes. The sequences of the corresponding genes were obtained, and probes were prepared by PCR using specific primer sets. The specificity of the probes was confirmed by cross PCR. The prepared probes were spotted on poly-L-lysine- or aminosilane-coated glass slides and hybridized with target DNA under several different conditions in order to determine the optimal hybridization temperature, glass-slide coating, and target cDNA concentration.

• Journal of Veterinary Science
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• v.21 no.1
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• pp.4.1-4.9
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• 2020

Fast and accurate detection of viral RNA pathogens is important in apiculture. A polymerase chain reaction (PCR)-based detection method has been developed, which is simple, specific, and sensitive. In this study, we rapidly (in 1 min) synthesized cDNA from the RNA of deformed wing virus (DWV)-infected bees (Apis mellifera), and then, within 10 min, amplified the target cDNA by ultra-rapid qPCR. The PCR products were hybridized to a DNA-chip for confirmation of target gene specificity. The results of this study suggest that our method might be a useful tool for detecting DWV, as well as for the diagnosis of RNA virus-mediated diseases on-site.

• KIEE International Transactions on Electrophysics and Applications
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• v.11C no.3
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• pp.85-90
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• 2001

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and other application area. So, the improvement of DNA detection system is very important for the determination of this hybridization reaction. In this study, we report the characterization of the probe and target oligonucleotide hybridization reaction using the evanescent field microscopy. First, we have fabricated DNA chip microarray. The particles which were immobilized oligonucleotides were arranged by the random fluidic self-assembly on the pattern chips, using hydrophobic interaction. Second, we have detected DNA hybridization reaction using evanescent field microscopy. The 5'-biotinylated probe oligonucleotides were immobilized on the surface of DNA chip microarray and the hybridization reaction with the Rhodamine conjugated target oligonucleotide was excited fluorescence generated on the evanescent field microscopy. In the foundation of this result, we could be employed as the basis of a probe olidonucleotide, capable of detecting the target oligonucleotide and monitoring it in a large analyte concentration range and various mismatching condition.

• Fisheries and Aquatic Sciences
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• v.5 no.1
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• pp.36-42
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• 2002

Microarrayer is used to make DNA chip and microarray that contain hundreds to thousands of immobilized DNA probes on surface of a microscope slide. This paper shows the develop-ment results for a printing type of microarrayer. It realizes a typical, low-cost and efficient microarrayer for generating low density micro array. The microarrayer is developed by using a prependicular type robot with three axes. It is composed of a computer-controlled three-axes robot and a pen tip assembly. The key component of the arrayer is the print-head containing the tips to immobilize cDNA, genomic DNA or similar biological material on glass surface. The robot is designed to automatically collect probes from two 96-well plates with up to 12 pens at the same time. To prove the performance of the developed microarrayer, we use the general water types of inks such as black, blue and red. The inks are distributed at proper positions of 96 well plates and the three color inks are immobilized on the slide glass under the operation procedure. As the result of the test, we can see that it has sufficient performance for the production of low integrated DNA chip consisted of 96 spots within $1cm^2$ area.