• Journal of Microbiology and Biotechnology
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• 제15권6호
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• pp.1377-1383
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• 2005

In a cDNA microarray experiment using Cy3 and Cy5 as labeling agents, particularly for the direct design, cDNAs from some genes incorporate one dye more efficiently than the other, which is referred to as the gene-specific dye bias. Dye-swaps, in which two dyes are switched on replicate arrays, are commonly used to control the gene-specific dye bias. We developed a simple procedure to extract the gene-specific dye bias information from a partial dye swap experiment. We detected gene-specific dye bias by identifying outliers in an X-Y plane, where the X axis represents the average log-ratio from two sets of dye swap pairs and the Y axis exhibits the average log ratio of four forward labeled arrays. We used this information for detecting differentially expressed genes, of which the additionally detected genes were validated by real-time RT-PCR.

• Nutritional Sciences
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• 제8권4호
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• pp.262-267
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• 2005

Reactive oxygen species can be generated in the skin by hair dyeing. The aim of this study was to find out the effects of the oxidative-type hair dye application in young women on the antioxidant systems. We investigated the lipid peroxide levels, glutathione (GSH) levels, and the antioxidant enzyme activities including superoxide dismutase (SOD), glutathione peroxidase (GSHPx) in plasma and erythrocytes and catalase (CAT) in erythrocytes, and DNA damages in lymphocytes. Also, plasma concentrations of antioxidant vitamins, vitamin A and E, were measured and the correlations between various antioxidant parameters and oxidative damages were evaluated The antioxidant enzyme activities in plasma (GSHPx) and in erythrocytes (SOD and CAT) were decreased significantly after hair dyeing. 1be lipid peroxide and GSH levels were not affected in both plasma and erythrocytes. No significant difference was found in the concentrations of both vitamin A and E between before and after hair dyeing. However, DNA damages expressed as the tail extent moment (TEM) and tail length (TL) were significantly (p<0.001) increased. The plasma vitamin E concentration was correlated with DNA damages (TEM: r=-0.590, p<0.01 and TL: r=-0.533. p<0.01) and RBC SOD activity (r=0.570, p<0.05). In turn, RBC SOD activity was significantly correlated with both plasma MDA levels (r=-0.412, p<0.05) and DNA damages (TM: r=-0.546, p<0.01, TL: r=-0.493, p<0.01). Our results demonstrated that the exposure to hair dyeing produced lymphocyte DNA damage and modification of the antioxidant enzyme activities. Also, there were very strong associations between plasma vitamin E concentration, RBC SOD activity and DNA damage induced by hair dyeing. It suggests that the antioxidant status of a subject is likely to be related to the extent of the harmful effects caused by hair dyeing.

• 한국미생물·생명공학회지
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• 제45권4호
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• pp.358-364
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• 2017

Asymmetric PCR preferentially amplifies one DNA strand for use in DNA hybridization studies. Linear-After-The-Exponential-PCR (LATE-PCR) is an advanced asymmetric PCR method which uses innovatively designed primers at different concentrations. This study aimed to optimise LATE-PCR parameters to produce single-stranded DNA of Candida spp. and Aspergillus spp. for detection via probe hybridisation. The internal transcribed spacer (ITS) region was used to design limiting primer and excess primer for LATE-PCR. Primer annealing and melting temperature, difference of melting temperature between limiting and excess primer and concentration of primers were optimized. In order to confirm the presence of single-stranded DNA, the LATE-PCR product was hybridised with digoxigenin labeled complementary oligonucleotide probe specific for each fungal genus and detected using anti-digoxigenin antibody by dot blotting. Important parameters that determine the production of single-stranded DNA in a LATE-PCR reaction are difference of melting temperature between the limiting and excess primer of at least $5^{\circ}C$ and primer concentration ratio of excess primer to limiting primer at 20:1. LATE-PCR products of Candida albicans, Candida parapsilosis, Candida tropicalis and Aspergillus terreus at up to 1:100 dilution and after 1 h hybridization time, successfully hybridised to respective oligonucleotide probes with no cross reactivity observed between each fungal genus probe and non-target products. For Aspergillus fumigatus, LATE-PCR products were detected at 1:10 dilution and after overnight hybridisation. These results indicate high detection sensitivity for single-stranded DNA produced by LATE-PCR. In conclusion, this advancement of PCR may be utilised to detect fungal pathogens which can aid the diagnosis of invasive fungal disease.

• 한국환경독성학회:학술대회논문집
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• 한국환경독성학회 2003년도 추계국제학술대회
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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.

• 약학회지
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• 제53권4호
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• pp.228-234
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• 2009

Topoisomerase I (Topo I) participates in the DNA replication, transcription, and repair. Binding of Topo I inhibitor to the Topo I-DNA cleavage complex forms stabilized ternary complex which blocks DNA religation and ultimately causes cell death. Camptothecin (CPT) and its derivatives have been among the most effective anticancer drugs by inhibition of topo I. However, efforts to synthesize non-CPT drugs have been actively going on because the CPT derivatives have several limitations such as poor solubility, short half-life, and side effects. As an indenoisoquinoline, NSC314622 is not as potent as CPT, but its chemical stability and slower reversibility of the cleavage complex made it a good lead compound. Recently, a series of indenoisoquinoline analogues were synthesized with substituted dimethoxy or methylenedioxy on the aromatic ring and alkylamino on the lactam nitrogen. Some of them showed quite good Topo I inhibitory activity. Using the computer docking program, Surflex-Dock, indenoisoquinoline analogues were docked into the human Topo I-DNA cleavable complex. The docking results showed that the compounds with activity better than NSC314622 intercalated between the -1 and +1 base pairs at the cleavage site, but those with little or no activities did not appear to intercalate. These results could be useful to design new Topo I inhibitors improved than CPT.

• Journal of Microbiology and Biotechnology
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• 제25권10호
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• pp.1714-1727
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• 2015

This work describes a new strategy for optimal design of Multiplex-PCR primer sequences. The process is based on the Particle Swarm Optimization-Simplex algorithm (Mult-PSOS). Diverging from previous solutions centered on heuristic tools, the Mult-PSOS is selfconfigured because it does not require the definition of the algorithm's initial search parameters. The successful performance of this method was validated in vitro using Multiplex-PCR assays. For this validation, seven gene sequences of the most prevalent bacteria implicated in urinary tract infections were taken as DNA targets. The in vitro tests confirmed the good performance of the Mult-PSOS, with respect to infectious disease diagnosis, in the rapid and efficient selection of the optimal oligonucleotide sequences for Multiplex-PCRs. The predicted sequences allowed the adequate amplification of all amplicons in a single step (with the correct amount of DNA template and primers), reducing significantly the need for trial and error experiments. In addition, owing to its independence from the initial selection of the heuristic constants, the Mult-PSOS can be employed by non-expert users in computational techniques or in primer design problems.

• 대한전기학회논문지:시스템및제어부문D
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• 제54권1호
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• pp.17-25
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• 2005

This paper provides sufficient conditions for the robustness of Affine linear TFM(Transfer Function Matrix) MIMO (Multi-Input Multi-Output) uncertain systems based on Rosenbrock's DNA (Direct Nyquist Array). The parametric uncertainty is modeled through a Affine TFM MIMO description, and the unstructured uncertainty through a bounded perturbation of Affine polynomials. Gershgorin's theorem and concepts of diagonal dominance and GB(Gershgorin Bands) are extended to include model uncertainty. For this type of parametric robust performance we show robustness of the Affine TFM systems using Nyquist diagram and GB, DNA(Direct Nyquist Array). Multiloop PI/PB controllers can be tuned by using a modified version of the Ziegler-Nickels (ZN) relations. Simulation examples show the performance and efficiency of the proposed multiloop design method.

• Journal of Preventive Medicine and Public Health
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• 제36권3호
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• pp.209-212
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• 2003

Because of advances of technologies in the field of genmic epidemiology in the recent years, specimen collection, storage and analysis became an essential part of research methodologies. DNA is now being used in epidemiologic studies to evaluate genetic risk factors and specimens other than the fresh whole blood can De used for PCR. Therefore, All nucleated cells, such as buccal swabs and urine specimens, are suitable for DNA analysis. For an unlimited source of genomic DNA, EBV transformation of lymphocytes can be used for immortalization. However, the type of specimen collected in genomic epidemiologic studies will depend on the study where the epidemiologist play a leading role for the design. We also briefly described various finds of analysis for SNP that is an essential part of the genomic epidemiology.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2002년도 봄 학술발표논문집 Vol.29 No.1 (B)
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• pp.160-162
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• 2002

SNP는 개인과 개인간의 DNA에 존재하는 한 염기 쌍의 차이(single base-pair variation)이다. SNP를 이용하면 사람마다 다른 유전병의 형태 등을 규명할 수 있다. 본 논문에서는 한국생명공학연구원의 유전체 사업단에서 개발해 오고 있는 웹기반 SNP데이터 검색 시스템의 설계와 구현에 대해서 설명한다. 본 시스템은 일반 속성(attribute)을 저장하고 검색하기 위해 PostgreSQL DBMS를 사용하고, DNA 시퀸스 검색을 위해 BLAST검색엔진을 사용한 약결합 아키텍쳐(loosely-coupled architecture)를 채택하고 있다. 즉, 일반 속성으로 저장될 수 있는 데이터들은 데이터베이스의 테이블들의 컬럼 값으로 저장하고 SQL 언어를 통해 검색할 수 있도록 하였으며, DNA 시퀸스 검색을 위해서는 BLAST에서 제공하는 인덱스를 구축하고 BLAST 명령어를 사용하여 검색할 수 있도록 하였다. 또한, 결과 분석 모듈을 구현하여 검색 결과들이 다른 웹 사이트의 데이터를 가리키도록 하였다.

• 대한전기학회:학술대회논문집
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• 대한전기학회 2000년도 하계학술대회 논문집 D
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• pp.3019-3021
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• 2000

In this paper. a new fuzzy modeling algorithm is proposed : it can express a given unknown system with a small number of fuzzy rules and be easily implemented. This method uses an independent array instead of a lattice form for a premise membership function. For the purpose of getting the initial value of fuzzy rules. the method uses the fuzzy c-means clustering method. To optimally tune the initial fuzzy rule. the DNA coding method is also utilized at same time. Box and Jenkins's gas furnace data is used to illustrate the validity of the proposed algorithm.