• 한국지진공학회:학술대회논문집
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• 한국지진공학회 2001년도 추계 학술발표회 논문집 Proceedings of EESK Conference-Fall 2001
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• pp.67-74
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• 2001

This paper presents the Safe Shutdown Earthquake(SSE) input motion for the seismic design of the Advanced Power Reactor 1400(APR1400). The Design Ground Response Spectra(DGRS) far the SSE is based on the design spectrum specified in regulatory Guide(RG) 1.60 of U.S. Nuclear Regulatory Commission(US NRC), anchored to a Peak Ground Acceleration(PGA) of 0.3g and enriched in the high frequency range. This SSE seismic input motion is to be applied to the seismic analysis as the free-field seismic motion at the ground surface of both the rock and generic soil sites fur APRI1400. The enrichment for APR1400 seismic input motion is performed considering the current US NRC regulations, the seismic hazard studies performed by the Lawrence Livermore National Laboratory (LINL) and Electric Power Research Institute(EPRI) for the Central and Eastern United States nuclear power plant sites, and the seismic input motions used in the design certifications of the three existing U.S. advanced standard plants. It is represented by a set of DGRS and the accompanying Target Power Spectral Density(PSD) Function in both the horizontal and vertical directions.

• BMB Reports
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• 제50권4호
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• pp.220-225
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• 2017

Antisense transcripts were initially identified as transcriptional noise, but have since been reported to play an important role in the quality control of miRNA functions. In this report, we tested the hypothesis that heterogeneous nuclear ribonucleoprotein K (hnRNPK) regulates miRNA function via competitive endogenous RNAs, such as pseudogenes, long non-coding RNAs, and antisense transcripts. Based on analyses of RNA sequencing data, the knockdown of hnRNPK decreased the antisense PTOV1-AS1 transcript which harbors five binding sites for miR-1207-5p. We identified heme oxygenase-1 (HO-1) mRNA as a novel target of miR-1207-5p by western blotting and Ago2 immunoprecipitation. The knockdown of hnRNPK or PTOV1-AS1 suppressed HO-1 expression by increasing the enrichment of HO-1 mRNA in miR-1207-5p-mediated miRISC. Downregulation of HO-1 by a miR-1207-5p mimic or knockdown of hnRNPK and PTOV1-AS1 inhibited the proliferation and clonogenic ability of HeLa cells. Taken together, our results demonstrate that hnRNPK-regulated PTOV1-AS1 modulates HO-1 expression via miR-1207-5p.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2016년도 춘계학술대회 및 임시총회
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• pp.17-17
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• 2016

Calcineurin governs stress survival, sexual differentiation, and virulence of the human fungal pathogen Cryptococcus neoformans. Herein, we identified and characterized calcineurin substrates in C. neoformans by employing phosphoproteomic $TiO_2$ enrichment and quantitative mass spectrometry. The identified targets include the zinc finger transcription factor Crz1 and proteins whose functions are linked to P-bodies/stress granules (PBs/SGs) and mRNA translation and decay, such as Pbp1 and Puf4. We show that Crz1 is a bona fide calcineurin substrate, and localization and transcriptional activity of Crz1 are controlled by calcineurin. Several of the calcineurin targets localized to PBs/SGs, including Puf4 and Pbp1, and are required for survival at high temperature and for virulence. Genetic epistasis analysis revealed that Crz1 and the novel targets Lhp1, Puf4, and Pbp1 function in a branched calcineurin pathway that orchestrates stress survival and virulence. These findings propose that calcineurin controls thermal stress and virulence at the transcriptional level via Crz1 and post-transcriptionally by regulating target factors involved in mRNA metabolism.

• Genomics & Informatics
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• 제16권4호
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• pp.29.1-29.5
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• 2018

Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments.

• Animal Bioscience
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• 제36권9호
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• pp.1336-1349
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• 2023

Objective: The study was conducted to screen differentially expressed miRNAs in sows at early pregnancy by high-throughput sequencing and explore its mechanism of action on embryo implantation. Methods: The blood serum of pregnant and non-pregnant Landrace×Yorkshire sows were collected 14 days after artificial insemination, and exosomal miRNAs were purified for high throughput miRNA sequencing. The expression patterns of 10 differentially expressed (DE) miRNAs were validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The qRT-PCR quantified the abundance of serum exosomal miR-192 in pregnant and control sows, and the diagnostic power was assessed by receiver operating characteristic (ROC) analysis. The target genes of DE miRNAs were predicted with bioinformatics software, and the functional and pathway enrichment analysis was performed on gene ontology and the Kyoto encyclopedia of genes and genomes terms. Furthermore, a luciferase reporter system was used to identify the target relation between miR-192 and integrin alpha 4 (ITGA4), a gene influencing embryo implantation in pigs. Finally, the expression levels of miRNAs and the target gene ITGA4 were analyzed by qRT-PCR, and western blot, with the proliferation of BeWo cells detected by cell counting kit-8 (CCK-8). Results: A total of 221 known miRNAs were detected in the libraries of the pregnant and non-pregnant sows, of which 55 were up-regulated and 67 were down-regulated in the pregnant individuals compared with the non-pregnant controls. From these, the expression patterns of 10 DE miRNAs were validated. The qRT-PCR analysis further confirmed a significantly higher expression of miR-192 in the serum exosomes extracted from pregnant sows, when compared to controls. The ROC analysis revealed that miR-192 provided excellent diagnostic accuracy for pregnancy (area under the ROC curve [AUC]=0.843; p>0.001). The dual-luciferase reporter assay indicated that miR-192 directly targeted ITGA4. The protein expression of ITGA4 was reduced in cells that overexpressed miR-192. Overexpression of miR-192 resulted in the decreased proliferation of BeWo cells and regulated the expression of cell cycle-related genes. Conclusion: Serum exosomal miR-192 could serve as a potential biomarker for early pregnancy in pigs. miR-192 targeted ITGA4 gene directly, and miR-192 can regulate cellular proliferation.

• 한국환경농학회지
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• 제34권2호
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• pp.69-76
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• 2015

국내 주요 국가산업단지인 여수국가산업단지, 울산국가산업단지 및 시화 반월산업단지 주변 토양에 대해서 2006년부터 2008년까지 3년 동안 상반기와 하반기로 각각 나누어 시료를 채취한 다음 중금속 농도와 분포특성을 파악하고, 부화지수를 이용한 토양 중금속 오염도를 평가하였다. 여수국가산업단지의 토양 중 Cd, Hg, Pb, Zn 및 Ni 농도가 다른 두 국가산업단지에서의 농도보다 더 높게 나타났으며, 시화 반월산업단지의 토양에서는 Cu, As 및 Cr의 농도가 높게 나타났으나 토양오염우려기준은 초과하지 않았다. 대체적으로 여수국가산업단지의 토양 중 중금속 오염이 다른 두 국가산업단지지역에 비하여 더 높게 나타난 것은 종합석유화학공업기지인 여수국가산업단지에는 입주해있는 석유화학공장들에서 발생하는 오염물질과 또한 이들을 수송하는 자동차 등의 비점오염원의 영향을 더 많이 받았기 때문인 것으로 판단되었다. 연구대상 지역별로 각각 구분하여 토양 중금속 결과를 이용한 주성분 분석결과 세 지역 모두 고유치가 1 이상인 주성분 2개를 각각 추출할 수 있었다. 여수 및 시화 반월국가산업단지에서는 Cd, Cu, Pb, Cr, Zn 및 Ni이 요인 1로, 그리고 As 및 Hg이 요인 2로 설명되었으며, 이는 두 지역 모두 석유화학과 기계, 철강, 전기전자 등의 배출원 영향을 받는 것으로 판단되었다. 울산국가산업단지은 Cd, Pb, Cr 및 Ni이 요인 1로, 그리고 Cu, As, Hg 및 Zn이 요인 2로 설명되었으며, 이는 기계, 석유화학, 운송장비, 비제조 등의 배출원 영향을 받는 것으로 판단되었다. 부화지수(EF)에 의한 오염도 평가 결과 3개 지역 모두 Cd, Pb 및 Zn의 EF값이 1 이상으로 나타나 이들 항목들의 오염개연성이 타 항목들에 비하여 높은 것으로 판단되었다. Cr은 시화 반월국가산업단지에서 1을 초과한 것으로 나타났으며, 3개 지역 모두 Zn의 부화지수가 상당히 높게 나타났다. 이상의 결과를 미루어 볼 때, 국가산업단지 토양의 중금속 오염은 토양환경 및 주변 농업환경에 악영향을 미칠 수 있으므로 다양한 중금속 배출원을 파악하여 각 배출원별로 철저한 관리가 필요할 것으로 판단된다.

• 한국세라믹학회지
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• 제51권5호
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• pp.472-476
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• 2014

In this work, a new method that utilizes L-cysteine salicylaldehyde Schiff-base modified macroporous polystyrene resin (PS-CSC) as an effective sorbent has been developed for preconcentration of trace cadmium and lead in environmental water samples. The effect of pH, the contact time, the elution conditions, the flow rate, the initial concentration of target metal ions, and the effects of interfering ions on the preconcentration of the analytes were investigated. The maximum adsorption capacity of PS-CSC under optimum conditions for cadmium and lead were found to be 6.03 - 18.17 mg/g and 12.58 - 36.13 mg/g when the initial concentration of metal ions between 5.0 - 90 mg/L. The limits of detection for cadmium and lead were 2.46 ng/L and $0.52{\mu}g/L$, with a preconcentration factor of 200. The developed method has been validated by analyzing certified reference material and successfully applied for the enrichment and determination of trace cadmium and lead from environmental water samples.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVI)
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• pp.88-92
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• 2005

Aptamer is the single-stranded oligonucleotide which binds to various target molecules such as proteins, peptides, lipids and small organic molecules with high affinity and specificity. DNA aptamers specific for the $17{\beta}-estradiol$ were selected by SELEX (Systematic Evolution of Ligands by EXponential enrichment) process from a random DNA library. These DNA aptamers have a high affinity to $17{\beta}-estradiol$ as an endocrine disrupting chemical. Nanowell and $200{\mu}m$ gold electrode were used as substrate for DNA aptamer immobilization and electrochemical analysis. Especially, nanowell gold electrode was fabricated by e-beam lithography. The size of single nanowell is 130nm and 40,000 nanowells were deposited on one gold electrode. The immobilization method was based on the interaction between the biotinylated aptamer and streptavidin deposited on gold electrode previously. Immobilization procedure was optimized by surface plasma resonance (SPR) and electrochemical analysis. After the immobilization of DNA aptamer on streptavidin modified gold electrode, $17{\beta}-estradiol$ solution was treated on aptamer immobilized gold electrode. The current of gold electrode was decreased by the binding of $17{\beta}-estradiol$ to DNA aptamer immobilized on gold electrode. However, in negative control experiments of 1-aminoanthraquinone and 2-methoxynaphthalene, the current was rarely decreased. And more sensitive data was obtained from nanowell gold electrode comparing with $200{\mu}m$ gold electrode.

• Journal of Microbiology and Biotechnology
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• 제25권10호
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• pp.1599-1605
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• 2015

The development of rapid and efficient genome sequencing methods has enabled us to study the evolutionary background of bacterial genetic information. Here, we present comparative genomic analysis of 17 Streptomyces species, for which the genome has been completely sequenced, using the pan-genome approach. The analysis revealed that 34,592 ortholog clusters constituted the pan-genome of these Streptomyces species, including 2,018 in the core genome, 11,743 in the dispensable genome, and 20,831 in the unique genome. The core genome was converged to a smaller number of genes than reported previously, with 3,096 gene families. Functional enrichment analysis showed that genes involved in transcription were most abundant in the Streptomyces pan-genome. Finally, we investigated core genes for the sigma factors, mycothiol biosynthesis pathway, and secondary metabolism pathways; our data showed that many genes involved in stress response and morphological differentiation were commonly expressed in Streptomyces species. Elucidation of the core genome offers a basis for understanding the functional evolution of Streptomyces species and provides insights into target selection for the construction of industrial strains.

• Toxicological Research
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• 제32권4호
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• pp.289-300
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• 2016

Non-genotoxic carcinogens are substances that induce tumorigenesis by non-mutagenic mechanisms and long term rodent bioassays are required to identify them. Recent studies have shown that transcription profiling can be applied to develop early identifiers for long term phenotypes. In this study, we used rat liver expression profiles from the NTP (National Toxicology Program, Research Triangle Park, USA) DrugMatrix Database to construct a gene classifier that can distinguish between non-genotoxic carcinogens and other chemicals. The model was based on short term exposure assays (3 days) and the training was limited to oxidative stressors, peroxisome proliferators and hormone modulators. Validation of the predictor was performed on independent toxicogenomic data (TG-GATEs, Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System, Osaka, Japan). To build our model we performed Random Forests together with a recursive elimination algorithm (VarSelRF). Gene set enrichment analysis was employed for functional interpretation. A total of 770 microarrays comprising 96 different compounds were analyzed and a predictor of 54 genes was built. Prediction accuracy was 0.85 in the training set, 0.87 in the test set and increased with increasing concentration in the validation set: 0.6 at low dose, 0.7 at medium doses and 0.81 at high doses. Pathway analysis revealed gene prominence of cellular respiration, energy production and lipoprotein metabolism. The biggest target of toxicogenomics is accurately predict the toxicity of unknown drugs. In this analysis, we presented a classifier that can predict non-genotoxic carcinogenicity by using short term exposure assays. In this approach, dose level is critical when evaluating chemicals at early time points.