• 생태와환경
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• 제54권3호
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• pp.170-189
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• 2021

환경유전자(eDNA)는 다양한 환경(수중, 토양, 대기)에 존재하는 생물체로부터 유래된 유전물질을 의미한다. eDNA는 높은 민감도, 짧은 조사시간 등 많은 장점들이 존재하며 이로 인해 생물 모니터링 및 유해생물과 멸종위기 생물을 탐색하는 분야에 다양하게 활용되고 있다. 이러한 eDNA를 채집하기 위해서는 대상생물 및 대상유전자뿐만 아니라 현장 여과방법 및 eDNA 보존방법과 같이 매우 다양한 항목들을 고려해야 한다. 특히 환경에서 eDNA를 채집하는 방법은 eDNA 농도와 직결되는 항목으로서 적절한 채집방법을 사용하여 eDNA를 채집할 때 정확한 분석결과를 얻을 수 있다. 또한 현장에서 채집한 eDNA를 보존하고 추출하는 과정에서도 정확한 방법을 사용하였을 때 현장에 분포하는 eDNA의 농도를 정확하게 파악할 수 있다. 특히 eDNA 연구를 시작하는 연구자들에게 eDNA 분야는 초기 진입 장벽이 매우 높은 기술로서 이를 위한 기초 자료가 매우 절실하다. 본 연구에서는 본 연구는 eDNA가 수생태계를 연구하기 위한 도구로서 보다 널리 이용되며, eDNA를 이용하기 시작하는 연구자들에게 도움을 주고자 수생태계에서 eDNA를 채집하고 및 운반하는 방법과 실험실에서 eDNA를 추출하는 방법을 소개하고, 보다 간편하고 효율적인 eDNA 채집 도구와 방법을 제시하였다.

• 전자공학회논문지
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• 제52권3호
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• pp.190-195
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• 2015

돌연변이 및 유전병의 원인이 되고 있는 유전자 단일염기 다형성(single nucleotide polymorphisms; SNPs) 검출은 조기진단, 치료 및 제약등 바이오관련 분야에서 매우 중요하다. SNPs 검출을 위한 방법은 다양하게 제시되고 있으나 상보적 DNA와 SNPs의 에너지 차이가 미세하여 SNPs 검출에는 많은 어려움이 존재한다. 본 논문에서는 SNPs를 검출하기 위하여 전하 검출형 전계효과 트랜지스터(field-effect transistors; FETs)를 이용하여 DNA가 가지고 있는 음전하 측정 방법으로 SNPs를 검출하였다. 상보적 DNA와 SNPs의 미세한 에너지 차이를 구분하기 위하여 타게트 DNA hybridization공정에서 드레인-소스 전극에 -0.3 V의 음전압을 인가하였다. 음전압 인가에 따라 DNA 자체 음전하와 센서 표면의 음전압의 전기적 반발력에 의해 센서에 검출되는 타게트 DNA hybridization 신호 크기는 감소하였으나 상보적 DNA와 SNPs의 신호 차는 1.7 mV에서 8.7 mV로 5배 이상 증가하여 검출되었다.

• Journal of Microbiology and Biotechnology
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• 제27권8호
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• pp.1367-1378
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• 2017

Epigenetic alterations such as DNA methylation, histone acetylation, and chromatin remodeling can control gene expression by regulating gene transcription. DNA methylation is one of the frequent epigenetic events that play important roles in cancer development. Cancer cells can gain significant resistance to anticancer drugs and escape programmed cell death through major epigenetic changes, including DNA methylation. To date, several research groups have identified instances of both (i) hypermethylation of tumor suppressor genes, and (ii) global hypomethylation of oncogenes. These changes in DNA methylation status could be used as biomarkers for the diagnosis and prognosis of cancer patients undergoing chemotherapies or other clinical therapies. Herein, we describe genes for which methylation is dependent upon anticancer drug resistance in patients with gastric cancer; we then suggest a significant epigenetic target to focus on for overcoming anticancer drug resistance.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
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• pp.29-44
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• 2001

DNA damage by physical insult including UV and g-radiation might provoke genetic alterations in cells, which is followed by either acute cell death or tumorigenesis. The responsiveness to g-radiation depends on cellular context of target cells. To understand the mechanisms of checkpoint control, repair and cell death following genotoxic stimu]i, cDNA microarray can provide the gene expression profile. To make a profile of gene expression in irradiated Jurkat T cells, we hybridized the cDNA microarray using cDNA from g-irradiated Jurkat T cells. Jurkat T cells were exposed to 4Gy to 16Gy, and total RNA were extracted at 4 to 24 hrs after irradiation. The hybridization of the microarray to fluorescence-labeled cDNA from treated and untreated cells was analyzed by bioinformatic analysis to address relative changes in expression levels of the genes present in the array. Responses varied widely in different time points, suggesting acute stress response and chronic restoration or cell death. From these results we could select 384 genes related to radiation response in Tcells, and radiation response might be different in various types of cells. Using Radchip, we could separate "the exposed" from control PBMCs. We propose that Radchip might be useful to check the radiation research as well as radiation carcinogenesis.

• Molecules and Cells
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• 제41권10호
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• pp.917-922
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• 2018

The CRISPR-Cas system is a well-established RNA-guided DNA editing technique widely used to modify genomic DNA sequences. I used the CRISPR-Cas9 system to change the second and third nucleotides of the triplet $T{\underline{CT}}$ of human TNSFSF9 in HepG2 cells to $T{\underline{AG}}$ to create an amber stop codon. The $T{\underline{CT}}$ triplet is the codon for Ser at the $172^{nd}$ position of TNSFSF9. The two substituted nucleotides, AG, were confirmed by DNA sequencing of the PCR product followed by PCR amplification of the genomic TNFSF9 gene. Interestingly, sequencing of the cDNA of transcripts of the edited TNFSF9 gene revealed that the $T{\underline{AG}}$ had been re-edited to the wild type triplet $T{\underline{CT}}$, and 1 or 2 bases just before the triplet had been deleted. These observations indicate that CRISPR-Cas9-mediated editing of bases in target genomic DNA can be followed by spontaneous re-editing (correcting) of the bases during transcription.

• 한국통신학회논문지
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• 제28권8C호
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• pp.803-810
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• 2003

본 논문은 여성 자궁경부암의 원인이 되는 인두유종 바이러스(papillomavirus)를 진단하기 위한 HPY-DNA 칩의 영상으로부터 탐촉자(probe)의 위치를 찾아내고 각 탐촉자에서의 교잡반응(hybridization) 여부를 결정하기 위한영상리 방법의 구현에 관한 것이다. HPV-DNA 칩은 22종의 HPV를 알아내기 위한 탐촉자들과 환자 샘플과 항상 반응하는 마커들로 구성되어 있다. 침 영상에서 탐촉자 들의 위치는 마커와 상대적으로 고정되어 있어서 도터(dotter)와 스캐너(scanner)의 정밀도에 따른 오차만을 갖는다. 한편 각 탐촉자는 진단신뢰도를 높이기 위하여 4번 씩 인쇄된다. 본 논문은 마커들간의 상대거리와 탐촉자의 중복 인쇄라는 사전정보를 템플릿 정합방법과 결합하여 안정적으로 마커를 찾고, 교잡반응 여부를 정확히 분류하는 방법을 제시한다. 정규화된 상관도를 정합도(matching measure)로 채택하여, 마커들의 상대적 위치에 대하여 평균을 취하면 안정적으로 마커를 찾을 수 있다는 것을 실험을 통하여 보인다. 또한 이미 계산된 정합도를 특징(feature) 값으로 사용하여 4개의 중복 탐촉자에 대한 평균 특징 값을 분류(classification)하면 탐촉자의 교잡반응 여부를 정확히 알아낼 수 있다는 실험 결과를 보인다.

• Journal of Microbiology and Biotechnology
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• 제21권2호
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• pp.183-186
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• 2011

Biochemical methods were selected to evaluate the role of exopolymeric substances in the stability of biofilms used in bioremediation processes. Biofilms of Thiomonas arsenivorans formed on pozzolana were thus treated with pronase (protein target), lectins (Con A or PNA), calcofluor or periodic acid (polysaccharides target), DNase (DNA target), and lipase (triglycerides target). Neither protease nor DNase treatments had any effect on bacterial adhesion. Lectins and calcofluor treatments mainly affected young biofilms. Lipase treatment had a noticeable effect on biofilm stability whatever the biofilm age. Results suggest that it would be an increased resistance of mature biofilms that protects them from external attacks.

• 통합자연과학논문집
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• 제6권1호
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• pp.57-63
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• 2013

Histone deacetylase (HDACs) is an enzyme family that deacetylates histones and non-histones protein. Availability of crystal structure of HDAC8 has been a boosting factor to generate target based inhibitors. Hydroxamic class is the most studied one to generate potent inhibitors. HDAC class I and class II enzymes are emerging as a therapeutic target for cancer, diabetes, inflammation and other diseases. DNA methylation and histone modification are epigenetic mechanism, is important for the regulation of cellular functions. HDACs enzymes play essential role in gene transcription to regulate cell proliferation, migration and death. The aim of this article is to provide a comprehensive overview about structure and function of HDACs enzymes, histone deacetylase inhibitors (HDACi) and HDACs enzymes as a therapeutic target for cancer, inflammation and diabetes.

• 대한약침학회지
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• 제19권1호
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• pp.37-44
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• 2016

Objectives: This study examined the relative efficacies of a derivative of betulinic acid (dBA) and its poly (lactide-co-glycolide) (PLGA) nano-encapsulated form in A549 lung cancer cells in vivo and in co-mutagen [sodium arsenite (SA) + benzo[a]pyrene (BaP)]-induced lung cancer in mice in vivo. Methods: dBA was loaded with PLGA nanoparticles by using the standard solvent displacement method. The sizes and morphologies of nano-dBA (NdBA) were determined by using transmission electron microscopy (TEM), and their intracellular localization was verified by using confocal microscopy. The binding and interaction of NdBA with calf thymus deoxyribonucleic acid (CT-DNA) as a target were analyzed by using conventional circular dichroism (CD) and melting temperature (Tm) profile data. Apoptotic signalling cascades in vitro and in vivo were studied by using an enzyme-linked immunosorbent assay (ELISA); the ability of NdBA to cross the blood-brain barrier (BBB) was also examined. The stage of cell cycle arrest was confirmed by using a fluorescence-activated cell-sorting (FACS) data analysis. Results: The average size of the nanoparticles was ~ 110 nm. Confocal microscopy images confirmed the presence of NdBA in the cellular cytoplasm. The bio-physical properties of dBA and NdBA ascertained from the CD and the Tm profiles revealed that NdBA had greater interaction with the target DNA than dBA did. Both dBA and NdBA arrested cell proliferation at G0/G1, NdBA showing the greater effect. NdBA also induced a greater degree of cytotoxicity in A549 cells, but it had an insignificant cytotoxic effect in normal L6 cells. The results of flow cytometric, cytogenetial and histopathological studies in mice revealed that NdBA caused less nuclear condensation and DNA damage than dBA did. TEM images showed the presence of NdBA in brain samples of NdBA fed mice, indicating its ability to cross the BBB. Conclusion: Thus, compared to dBA, NdBA appears to have greater chemoprotective potential against lung cancer.

• Biotechnology and Bioprocess Engineering:BBE
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• 제9권2호
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• pp.93-99
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• 2004

Pathogens pose a significant threat to humans, animals, and plants. Consequently, a considerable effort has been devoted to developing rapid, convenient, and accurate assays for the detection of these unfavorable organisms. Recently, DNA-microarray based technology is receiving much attention as a powerful tool for pathogen detection. After the target gene is first selected for the unique identification of microorganisms, species-specific probes are designed through bioinformatic analysis of the sequences, which uses the info rmation present in the databases. DNA samples, which were obtained from reference and/or clinical isolates, are properly processed and hybridized with species-specific probes that are immobilized on the surface of the microarray for fluorescent detection. In this study, we review the methods and strategies for the development of DNA microarray for pathogen detection, with the focus on probe design.