• 자연과학논문집
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• 제9권1호
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• pp.19-24
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• 1997

PCR 방법을 이용하여 K11 RNA 중합효소를 coding하는 Klebsiella phage gene 1을 cloning 하였고 lac 전사촉진제 조절 하에 발현시켰다. K11 RNA 중합효소는 DAEA-sephacel과 Affigel blue column chromatographies를 사용하는 상용 방법으로 분리하였다. DAEA-sephacel의 0.2-0.3 M $NH_4Cl$ 분획에서 K11 RNA 중합효소의 활성을 보였고, 다음 단계의 Affigel blue column에서 SDS-polyacryl amide gel 상의 단일 band로 분리되었다. K11 RNA 중합효소는 T7 그룹 phage RNA 중합효소로 다른 T7 그룹phage RNA 중합효소와 많은 상동성을 보인다. (대장균 phage T7, T3과 Salmonella tyhimurium phage SP6 RNA 중합효소). 이미 우리는 T7과 SP6 전사촉진제 변이체를 제조한 바 있고 T7과 SP6 RNA 중합효소의 전사촉진제 특이성을 연구한 바 있다 (이상수와 강창원, 1993). K11 RNA 중합효소의 전사촉진제 특이성을 알아보기 위해 SP6 전사촉진제 변이체를 사용하여 in vitro K11 RNA 중합효소의 활성을 측정하였다. 이 변이체 중 K11 전사촉진제와 가장 유사한 것이 가장 높은 K11 RNA 중합효소 활성을 보였다.

• 미생물학회지
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• 제41권2호
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• pp.117-124
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• 2005

Rotifer와 병든 넙치 자어로부터 분리된 2개의 균주는 표현형적인 특성 확인 결과 Vibrio ichthyoenteri로 확인이 되었다. V. ichthyoenteri를 검출하기 위래 고감도 PCR 방법 개발을 하기 위래 V. ichthyoenteri 16S-23S rRNA intergenic spacer region(ISR)을 분석하였고, V. ichthyoenteri중 특이적 primer를 개발하였다. V. ichthyoenteri 의 ISR를 분석한 결과 1개의 다형성 ISR type서열을 포함하고 있었다. ISR서열은 길이는 348bp이며 tRNA gene을 가지고 있지 않았다. 이 서열을 가지고 이미 알려진 다른 Vibrio 종의 ISR 서열과 mutiple alignment를 수행한 결과 여러 영역에서 높은 가변성을 나타내어 가변 부위를 표적으로 하여 V. ichthyoenteri를 검출하기 위한 종 특이적 primer를 제작하였다. 제작된 primer의 특이성을 확인하기 위해 Vibrio 표준균주 19종의 genomic DNA와 분리균주 18 group에 genomic DNA 그리고 V. ichthyoenteri와 가장 유사한 서열을 가지고 있다고 알려진 Vibrio 종의 genomic DNA를 가지고 시험하였다. 그 결과 본 연구에서 제작된 종 특이적 primer를가지고 PCR 반응을 하면 V. ichthyoenteri를 검출 할 수가 있다.

• Bulletin of the Korean Chemical Society
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• 제26권9호
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• pp.1385-1389
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• 2005

Human hepatitis B virus (HBV) is a pathogen related to the development of liver diseases including chronic hepatitis, cirrhosis, and hepatocellular carcinoma (HCC). However, the efficient methods to suppress HBV replication have not been developed yet. Therefore, we have used RNA interference (RNAi) as a potential tool for the suppression of HBV replication. Here, we designed a 21 nt small intefering dsRNA (siRNA) against hepatitis B virus X (HBx) RNA with 3' overhanging ends derived from T7 promoter. It has been reported that HBV X protein plays an important role in HBV gene expression and viral replication. The suppression of HBx gene expression by the 21 nt siRNA was investigated by Northern blot analysis and chloramphenicol acetyl transferase (CAT) assay. The level of HBx mRNA was decreased by siRNA in a dose-dependent manner. We also found that the 21 nt siRNA inhibited the HBV replication in hepatocellular carcinoma cell.

• Genomics & Informatics
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• 제18권3호
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• pp.26.1-26.6
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• 2020

Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type-specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

• Journal of Korean Neurosurgical Society
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• 제65권5호
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• pp.697-709
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• 2022

Objective : The present study aimed to identify the function of ischemic stroke (IS) patients' peripheral blood and its role in IS, explore the pathogenesis, and provide direction for clinical research progress by comprehensive bioinformatics analysis. Methods : Two datasets, including GSE58294 and GSE22255, were downloaded from Gene Expression Omnibus database. GEO2R was utilized to obtain differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the database annotation, visualization and integrated discovery database. The protein-protein interaction (PPI) network of DEGs was constructed by search tool of searching interactive gene and visualized by Cytoscape software, and then the Hub gene was identified by degree analysis. The microRNA (miRNA) and miRNA target genes closely related to the onset of stroke were obtained through the miRNA gene regulatory network. Results : In total, 36 DEGs, containing 27 up-regulated and nine down-regulated DEGs, were identified. GO functional analysis showed that these DEGs were involved in regulation of apoptotic process, cytoplasm, protein binding and other biological processes. KEGG enrichment analysis showed that these DEGs mediated signaling pathways, including human T-cell lymphotropic virus (HTLV)-I infection and microRNAs in cancer. The results of PPI network and cytohubba showed that there was a relationship between DEGs, and five hub genes related to stroke were obtained : SOCS3, KRAS, PTGS2, EGR1, and DUSP1. Combined with the visualization of DEG-miRNAs, hsa-mir-16-5p, hsa-mir-181a-5p and hsa-mir-124-3p were predicted to be the key miRNAs in stroke, and three miRNAs were related to hub gene. Conclusion : Thirty-six DEGs, five Hub genes, and three miRNA were obtained from bioinformatics analysis of IS microarray data, which might provide potential targets for diagnosis and treatment of IS.

• 식물조직배양학회지
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• 제27권5호
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• pp.379-385
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• 2000

tRNA and 7SL RNA based antisense vehicles were prepared by inserting conserved anti-viral and anti-viroid domains. Anti-PVS coat protein leader sequence (ACPL) and antistructural antihairpin domain of PSTVd (AHII) were inserted in tRNA cassette; anti- zing finger domain of PVS, AHII and anti hop latent viroid ribozyme were inserted in 7SL RNA gene isolated from A. thaliana. These constructs were shown to be transcribed both, in in vitro and in in vivo conditions. However, it followed from our work that closely linked position of PoIII reference genes and PoIIII antisense genes within T-DNA lead to the impairment of RNA expression in transgenic plants. To assay in vivo transcription of antisense genes, hairy root potato cultures were established using h. tumefaciens A4-24 bearing both, Ri plasmid and PoIII-promoterless plant expression vectors with antisense RNA genes. Expression of antisense RNA in transgenic potato tissues was proven by specific RT-PCR reactions.

• International Journal of Industrial Entomology and Biomaterials
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• 제2권1호
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• pp.1-6
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• 2001

This paper reports a few characteristics of seven insect mitochondrial genomes sequenced completely (Bombyx mori, Drosophila melanogaster, D. yakuba, Apis mellifera, Anopheles gambiae, A. quadrimaculatus, and Locusta migratoria). Comparative analysis of complete mt genome sequences from several species revealed a number of interesting features (base composition, gene content, A+T-rich region, and gene arrangement, etc) of insect mitochondrial genome. The properties revealed by our work shed new light on the organization and evolution of the insect mitochondrial genome and more importantly open up the way to clearly aimed experimental studies for understanding critical roles of the regulatory mechanisms (transcription and translation) in mitochondrial gene expression.

• Journal of Plant Biotechnology
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• 제44권1호
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• pp.89-96
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• 2017

CRISPR/Cas9 기술은 생명공학을 활용한 신품종 작물육성에 있어 패러다임 변혁을 가져다 줄 핵심 기반기술이다. 본 연구에서는 CRISPR/Cas9를 이용하여 유전자편집기술을 기존에 알려진 방법보다 쉽고 정확하게 실험 할 수 있도록 sgRNA 디자인, 벡터구축, 형질전환체 육성 및 분석 등을 자세히 기술하였다. sgRNA는 http://www.rgenome.net/ 사이트에서 NGG 영역을 중심으로 하여 target-up: 5'-ggcaGNNNNNNNNNNNNNNNNNNNN-3'과 target-down: 5'-aaacNNNNNNNNNNNNNNNNNNNNC-3'의 올리고를 디자인하였다. 식물형질전환용 벡터는 pPZP-Cas9-RGEN을 기본으로 하였으며, sgRNA의 프로모터는 OsU3를 이용하여 pPZP::35S::Cas9::PinII-OsU3::sgRNA::Bar-Gen 순으로 구축하였다. 형질전환체의 육성은 단기형질전환 Agrobacterium 법을 사용하였으며 재분화 식물체를 얻는데48일 정도 소요되었다. 형질전환체 유무는 genomic PCR 분석으로 single copy 선발은 TaqMan PCR로 분석하였다. 정밀유전자편집 식물체는 T1 세대에서 T-DNA 삽입되지 않은 식물체를 Bar-strip에 의해 선발하였다. 선발된 식물체의 sgRNA 영역의 염기배열 조사에 의해 유전자 편집 식물체를 육성하였다. 따라서 본 연구에서 CRISPR/Cas9 system에 의한 정밀유전자편집 기술을 이용하여 보다 빠르고 쉽고 경제적으로 유전자가 편집된 개체를 확보할 수 있었다. 본 실험에서 확립된 system은 상업용 식물 계통육성에 이용 가능하여 육종적 가치가 매우 클 것으로 사료된다.

• BMB Reports
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• 제28권6호
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• pp.509-514
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• 1995

A putative secondary structure of the mRNA for the human hepatitis B virus (HBV) X gene is proposed based on not only chemical and enzymatic determination of its single- and double-stranded regions but also selection by the computer program MFOLD for energy minimum conformation under the constraints that the experimentally determined nucleotides were forced or prohibited to base pair. An RNA of 536 nucleotides including the 461-nucleotide HBV X mRNA sequence was synthesized in vitro by the phage T7 RNA polymerase transcription. The thermally renatured transcripts were subjected to chemical modifications with dimethylsulfate and kethoxal and enzymatic hydrolysis with single strand-specific RNase T1 and double strand-specific RNase V1, separately. The sites of modification and cleavage were detected by reverse transcriptase extension of 4 different primers. Many nucleotides could be assigned with high confidence, twenty in double-stranded and thirty-seven in Single-stranded regions. These nucleotides were forced and prohibited, respectively, to base pair in running the recursive RNA folding program MFOLD. The results suggest that 6 different regions (5 within X mRNA) of 14~23 nucleotides are Single-stranded. This putative structure provides a good working model and suggests potential target sites for antisense and ribozyme inhibitors and hybridization probes for the HBV X mRNA.

• 미생물학회지
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• 제55권3호
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• pp.303-305
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• 2019

섬 해안가 토양에서 방선균주 Gordonia sp. MMS17-SY073를 분리하여 유전체 분석을 실시하였고, 그 결과 5,962,176 염기쌍 및 67.4%의 G + C 함량으로 이루어진 유전체 정보를 확보하였다. 유전정보 분석 결과 총 5,201개 단백질 지정 유전자, 6개 rRNA 유전자 및 45개 tRNA 유전자를 확인하였다. MMS17-SY073 균주는 16S rRNA 유전자를 이용한 분석 결과 분류학적으로 Gordonia soli의 표준균주와 가장 가까웠으며 그 유사도는 98.5%로 나타났다. MMS17-SY073 균주는 non-ribosomal peptide synthetase 유형을 비롯한 다수의 이차대사산물 생합성 유전자를 보유하고 있는 것으로 나타났다.