• 반도체디스플레이기술학회지
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• 제15권1호
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• pp.27-32
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• 2016

A new lane detection algorithm is proposed for the analysis of DNA fingerprints from a polymerase chain reaction (PCR) gel electrophoresis image. Although several research results have been previously reported, it is still challenging to extract lanes precisely from images having abrupt background brightness difference and bent lanes. We propose an edge based algorithm for calculating the average lane width and lane cycle. Our method adopts sub-pixel algorithm for extracting rising-edges and falling edges precisely and estimates the lane width and cycle by using k-means clustering algorithm. To handle the curved lanes, we partition the gel image into small portions, and track the lane centers in each partitioned image. 32 gel images including 534 lanes are used to evaluate the performance of our method. Experimental results show that our method is robust to images having background difference and bent lanes without any preprocessing.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2017년도 춘계학술발표대회
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• pp.577-580
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• 2017

중합 효소 연쇄 반응 (PCR) 젤 전기영동 이미지에서 DNA 지문을 분석하기 위한 새로운 레인 검출 및 추적 알고리즘이 제안하였다. 이전에 여러 연구 결과가 보고되었지만 갑작스런 배경 밝기 차이와 구부러진 레인이 있는 이미지에서 레인을 정확하게 추출하는 것은 여전히 어려움이 있다. 우리는 평균 레인 폭과 레인 주기를 계산하기 위한 에지 기반 알고리즘을 제안한다. 본 논문에서 제안한 방법은 k-means 클러스터링 알고리즘을 이용하여 상승 에지와 하강 에지를 정확하게 추출하는 부화소(sub-pixel) 알고리즘을 적용하여 레인 폭과 주기를 추정한다. 구부러진 레인을 처리하기 위해 젤 이미지를 정상영역과 비정상영역으로 분할하고, 각 분할 된 이미지의 레인 중심을 추적한다. 우리가 제안한 방법의 성능을 평가하기 위해 534 레인을 포함한 32 개의 젤 이미지가 사용되었다. 실험 결과는 우리의 방법이 전처리 과정 없이 배경 차이와 구부러진 레인을 갖는 이미지에 강인함을 보여 주었다.

• 환경생물
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• 제22권1호
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• pp.213-219
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• 2004

동굴 내 정점별 세균 군집 구조를 분석하기 위하여 PCf amplified 16S rDNA denaturing gradient gel electrophoresis(DGGE)를 적용하였다. DGGE는 동일한 분자량을 갖는 dsDNA band라고 할지라도, 각각의 염기서열 차이에 따라 전기영동 상에서 고유한 band양상을 나타낼 수 있다. eubacteria의 16S rDNA V3region을 증폭하기 위해 GC341F와 PRUN518r을 primer로 사용하여 지하수내에 미생물 군집의 다양성과 유사성을 분석하였다. DGGE band 양상을 통해 동굴내의 세균 군집 구조는 외부 환경에 비해 상대적으로 종다양성이 낮으며 동굴내 에서 특이적으로 서식하는 종이 있음을 확인하였다. 또한 유기 영양물질의 공급이 제한되어 있는 동굴에서 구아노가 주요 유기 영양물질의 공급원으로서 큰 영향을 미치고 있는 것으로 파악되었다. DGGE 상의 일부 band의 염기서열분석 결과 Pseudomonas sp. NZ060과 Pseudomonas pseudoalcaligenes, uncultured Variovorax sp., soil bacterium NS7로 동정되었다.

• BMB Reports
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• 제40권6호
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• pp.853-860
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• 2007

Resistance to anticancer drugs is a major obstacle in the effective treatment of tumors. To understand the mechanisms responsible for multidrug resistance (MDR), a proteomic approach was used to identify proteins that were expressed in different levels by the adriamycinresistant human gastric cancer cell line, SGC7901/ADR, and its parental cell line, SGC7901. Two-dimensional gel electrophoresis (2-DE) and image analysis was used to determine which protein spots were expressed in different levels by the two cell lines. These spots were then partially identified using ESI-Q-TOF mass spectrometry, and the differential expressional levels of the partially identified proteins were then determined by western blot analysis and real-time RT-PCR. Additionally, the association of Nucleophosmin (NPM1), a protein that was highly expressed by SGC7901/ADR, with MDR was analyzed using siRNA. As a result of this study, well-resolved, reproducible 2-DE patterns of SGC7901/ADR and SGC7901 were established, and 16 proteins that may playa role in the development of thermo resistance were identified. Additionally, suppression of NPMl expression was found to enhance adriamycin chemosensitivity in SGC7901/ADR. These results provide a fundamental basis for the elucidation of the molecular mechanism of MDR, which may assist in the treatment of gastric cancer.

• Journal of Animal Science and Technology
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• 제45권6호
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• pp.911-916
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• 2003

돼지 Duroc 품종의 mitochondria DNA D-loop전체 유전자를 증폭하기 위하여 많은 동물에서 고도로 상동성이 높은 tRNA-Pro와 tRNA-Phe 염기서열 일부를 이용하여 oligonucleotide primer를 제작하였다. 그 결과 Duroc 품종의 D-loop 전체 유전자는 1,145 base pairs 였으며, 그 중간위치에 10bp의 Sus Scrofa-specific sequence (TACACGTGCG)가 10개 존재하고 있었다. 돌연변이 검출을 위하여 가장 변이가 심한 지역을 primer 제작하여 345 bp의 DNA 단편을 증폭하였으며, Single Stranded Conformation Polymorphism(SSCP) 분석은 8% polyacrylamide gel에서 200 V, 16시간 전기영동하여 ethidium bromide (EtBr)로 10분간 염색하여 UV image analyzer로 관찰하였다. 그 결과 두 개의 서로 다른 밴드유형을 관찰하였으며, 21개 부위에서 염기서열 변이가 관찰되었다. 이러한 결과는 유전적 다양성 변이를 검출하는데 SSCP 분석이 유용한 도구라고 사료된다.

• Archives of Plastic Surgery
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• 제34권6호
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• pp.679-684
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• 2007

Purpose: DMH(1,2-dimethylhydrazine) has been known to induce vascular neoplasm such as malignant endothelioma in animal experiment, through induction of abnormal proliferation of HUVECs. In our previous studies, 11 types of PKC isoenzymes were determined by RT-PCR and the expression of $PKC{\alpha}$, and ${\mu}$ was more prominent than other PKC isoenzymes in the DMH-treated group. However, this result was not based on objective assessment. In this study, we further evaluated the role of $PKC{\alpha}$ on the DMH-induced abnormal proliferation of HUVECs by two different methods to identify its presence with high relevance in objective view. $PKC{\mu}$ will be investigated in further study. Methods: The study was conducted with the cultured HUVECs group(control) and the $0.75{\times}10^{-9}M$ DMH-treated group. After processing protein extraction in 0 and 24 hour, extracted protein was treated of quantitative test through BCA protein assay. In the western blot analysis, electrophoresis was performed in the order of gel preparation, sample preparation, and gel running. Electrotransfer to nitrocellulose membrane and reaction with antibody were done. Detection of $PKC{\alpha}$ was achieved through "Gel Image Analysis System". In the fluorescence immunocytochemical analysis, the grading of radiance of the intracellular $PKC{\alpha}$ particles was detected with confocal microscope after treating with primary and fluorescent secondary antibody in 0 and 24 hours. Results: The Western blot analysis showed increased $PKC{\alpha}$ expression from the specimen obtained in 24 hour of the DMH treatment group when compared to those in control group. Under confocal fluorescence microscope, the emitting radiance in the DMH treated group was brighter at 24 hours as well. Conclusion: We believe that $PKC{\alpha}$ plays a role in DMH-induced abnormal proliferation of the vascular endothelium, which may provide insights in understanding the vascular neoplasm.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제32권1호
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• pp.8-18
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• 2006

Purpose: The purpose of this study was to verify that the expressions of angiogenin, transforming growth factor-beta(TGF-${\beta}$), vascular endothelial growth factor(VEGF), human apurinic/apyrimidinic endonuclease(APEX) and tumor necrosis factor-alpha(TNF-${\alpha}$) were associated with the tumorigenesis of the oral squamous cell carcinoma(OSCC). Materials and Methods: Fifty-one samples of OSCC and fifteen normal oral mucosae were obtained to analyze the expression levels of above five factors. mRNA expressions were quantified by the quantitative competitive PCR(QC-PCR) method. After 2% agarose gel electrophoresis stained with ethidium bromide, the concentration of mRNA was calculated by a digital image analysis system. The expression levels of angiogenin, TGF-${\beta}$, VEGF, APEX and TNF-${\alpha}$ were compared by unpaired Student's t-tests between cancer and normal tissues. We analyzed statistically to find the cut-off values that would be useful as diagnostic markers, and the linear regression analysis between every two factors of these five factors by SAS system. Results: All of these five factors (angiogenin: P<0.0037, TGF-${\beta}$: P<0.0001, VEGF: P<0.0102, APEX: P<0.0023, TNF-${\alpha}$: P<0.0074) were significantly correlated with OSCC. In the analysis to find the cut-off values for the diagnosis, we could not find any value that had a reasonable sensitivity and specificity. In the linear regression analysis, there were correlations between angiogenin and TNF-${\alpha}$, TGF-${\beta}$ and VEGF, TGF-${\beta}$ and APEX, TGF-${\beta}$ and TNF-${\alpha}$, VEGF and APEX, VEGF and TNF-${\alpha}$, APEX and TNF-${\alpha}$. Conclusion: Our results suggest that not only angiogenin, TGF-${\beta}$, VEGF, APEX and TNF-${\alpha}$ are significantly associated with the tumorigenesis, but also the close relationship between these factors might enhance the tumorigenesis of OSCC. We can not find clinical availability for diagnosis.