• Molecules and Cells
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• 제44권11호
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• pp.843-850
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• 2021

The rapid increase in collateral omics and phenotypic data has enabled data-driven studies for the fast discovery of cancer targets and biomarkers. Thus, it is necessary to develop convenient tools for general oncologists and cancer scientists to carry out customized data mining without computational expertise. For this purpose, we developed innovative software that enables user-driven analyses assisted by knowledge-based smart systems. Publicly available data on mutations, gene expression, patient survival, immune score, drug screening and RNAi screening were integrated from the TCGA, GDSC, CCLE, NCI, and DepMap databases. The optimal selection of samples and other filtering options were guided by the smart function of the software for data mining and visualization on Kaplan-Meier plots, box plots and scatter plots of publication quality. We implemented unique algorithms for both data mining and visualization, thus simplifying and accelerating user-driven discovery activities on large multiomics datasets. The present Q-omics software program (v0.95) is available at http://qomics.sookmyung.ac.kr.

• Environmental Analysis Health and Toxicology
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• 제31권
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• pp.16.1-16.9
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• 2016

Objectives Banha-sasim-tang (BST), which consists of seven different herbs, is one of the most popular herbal formulae for treating gastrointestinal disorders in Eastern Asia. The commonly used herbal medicine is often co-administered with other therapeutic drugs, which raises the possibility of herb-drug interactions and may modify the clinical safety profile of therapeutic drugs. Methods We investigated the potential herb-drug interactions between BST extract and midazolam (MDZ) in mice. The area under the plasma concentration-time curve (AUC) of MDZ and 1'-hydroxymidazolam (1'-OH-MDZ) was evaluated for both oral and intraperitoneal administration of MDZ, following oral administration of BST (0.5 and 1 g/kg). Results It was found that the AUC of MDZ and 1'-OH-MDZ was lower in case of oral administration of MDZ. Administration of BST extract was not associated with hepatic cytochrome P450 activity. BST extract induced a strong reduction in pH and it has been reported that oral mucosal absorption of MDZ is lower at low pH. The decreased absorption rate of MDZ might be caused by the ingredients of BST and may not be related to other factors such as increased excretion of MDZ by P-glycoprotein. Conclusions The altered pharmacokinetics of midazolam caused by co-administration with BST in vivo could be attributed to a decrease in pH and subsequent reduction of MDZ absorption rate.

• Toxicological Research
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• 제34권1호
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• pp.23-29
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• 2018

Ethanol-induced fat accumulation, the earliest and most common response of the liver to ethanol exposure, may be involved in the pathogenesis of liver diseases. Isoliquiritigenin (ISL), an important constituent of Glycyrrhizae Radix, is a chalcone derivative that exhibits antioxidant, anti-inflammatory, and phytoestrogenic activities. However, the effect of ISL treatment on lipid accumulation in hepatocytes and alcoholic hepatitis remains unclear. Therefore, we evaluated the effect and underlying mechanism of ISL on ethanol-induced hepatic steatosis by treating AML-12 cells with 200 mM ethanol and/or ISL ($0{\sim}50{\mu}M$) for 72 hr. Lipid accumulation was assayed by oil red O staining, and the expression of sirtuin1 (SIRT1), sterol regulatory element-binding protein-1c (SREBP-1c), AMP-activated protein kinase (AMPK), and peroxisome proliferator-activated receptor alpha ($PPAR{\alpha}$) was studied by western blotting. Our results indicated that ISL treatment upregulated SIRT1 expression and downregulated SREBP-1c expression in ethanol-treated cells. Similarly, oil red O staining revealed a decrease in ethanol-induced fat accumulation upon co-treatment of ethanol-treated cells with 10, 20, and $50{\mu}M$ of ISL. These findings suggest that ISL can reduce ethanol induced-hepatic lipogenesis by activating the SIRT1-AMPK pathway and thus improve lipid metabolism in alcoholic fatty livers.

• Journal of Microbiology and Biotechnology
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• 제18권8호
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• pp.1357-1363
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• 2008

The $P_{entC}$ promoter of the entCERA operon encoding enzymes for enterobactin biosynthesis in Escherichia coli is tightly regulated by the availability of iron in the culture medium. In iron-rich conditions, the $P_{entC}$ promoter activity is strongly repressed by the global transcription regulator Fur (ferric uptake regulator), which complexes with ferrous ions and binds to the Fur box 19-bp inverted repeat. In this study, we have constructed the expression vector pOS2 containing the $P_{entC}$ promoter and characterized its repression, induction, and modulation by quantifying the expression of the lacZ reporter gene encoding $\beta$-galactosidase. $\beta$-Galactosidase activities of E. coli transformants harboring pOS2-lacZ were highly induced in the presence of divalent metal ion chelators such as 2,2'-dipyridyl and EDTA, and were strongly repressed in the presence of excess iron. It was also shown that the basal level $\beta$-galactosidase expression by the $P_{entC}$ promoter was drastically decreased by incorporating the fur gene into the expression vector. Since the newly developed iron chelator-inducible expression system is efficient and cost-effective, it has wide applications in recombinant protein production.

• 생태와환경
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• 제51권1호
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• pp.16-28
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• 2018

남조류에 대한 오랜 연구로 많은 사실을 알게 되었음에도 여전히 미지의 영역으로 남아있는 부분이 많은데, 분자 생물학에 기반한 오믹스 기술의 발전으로 새로운 도구를 이용한 다른 관점에서의 연구가 최근 활발해지고 있다. 일차적으로는 유전체 염기서열 분석기술을 사용하여 다양한 남조류의 유전체 비교분석과 유전자의 발현 양상을 연구함으로써, 독소 합성의 조절 기작 등 생리적 특성이 나타나는 원리 규명에 많은 노력이 기울여지고 있다. 또한 남조류 유전형의 다양성과 이들이 밀접하게 상호작용하는 박테리아 군집이 계절적 및 환경적 요인에 어떻게 반응하여 변화하고, 이러한 변화가 생태계에는 어떤 영향을 미치는지에 대한 연구가 생물정보학 분석기법과 결합하면서, 생태계의 복잡한 작동방식에 대한 이해도 늘어나고 있다. 특히 다양한 오믹스 기법을 복합 적용함으로써 생태계 안에서 일어나는 모든 층위의 생물학적 반응에 대한 총체적 그림을 그리는 것이 현실화되고 있으며, 이렇게 그려진 설계도로부터 녹조를 효과적으로 제어하고 건강한 수생태계를 유지할 수 있는 새로운 통찰의 가능성에 대한 기대가 고조되고 있다.

• Mass Spectrometry Letters
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• 제10권2호
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• pp.61-65
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• 2019

Korean ginseng (Panax ginseng Meyer) is a traditional herb used across the world to treat various diseases. Although, red ginseng is this herb's most famous product and has demonstrated diverse pharmacological activities, white ginseng (WG) is another ginseng product that is made fresh and individually regulated in Eastern Asia. Red and white ginseng show different characteristics due to distinct processing steps despite originating from the same plant, and the drug interactions induced by WG have not been well documented. Selegiline is a selective monoamine oxidase (MAO) inhibitor used as an antidyskinetic and antiparkinsonian agent. Here we developed a quantification method for selegiline in mouse plasma using a C8 stationary phase in triple quadrupole-mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM). The validated LC-MS/MS method was successfully applied to determine the potential interaction with WG extract (0.1 g/kg/day) pre-administered for 4 weeks. The $AUC_{0-240min}$ of selegiline was altered due to a decrease in the absorption of selegiline with repeated administration of WG extract.

• BMB Reports
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• 제55권6호
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• pp.281-286
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• 2022

Hepatocellular carcinoma is a major health burden, and though various treatments through much research are available, difficulties in early diagnosis and drug resistance to chemotherapy-based treatments render several ineffective. Cancer stem cell model has been used to explain formation of heterogeneous cell population within tumor mass, which is one of the underlying causes of high recurrence rate and acquired chemoresistance, highlighting the importance of CSC identification and understanding the molecular mechanisms of CSC drivers. Extracellular CSC-markers such as CD133, CD90 and EpCAM have been used successfully in CSC isolation, but studies have indicated that increasingly complex combinations are required for accurate identification. Pseudogene-derived long non-coding RNAs are useful candidates as intracellular CSC markers - factors that regulate pluripotency and self-renewal - given their cancer-specific expression and versatile regulation across several levels. Here, we present the use of microarray data to identify stemness-associated factors in liver cancer, and selection of sole pseudogene-derived lncRNA ZNF204P for experimental validation. ZNF204P knockdown impairs cell proliferation and migration/invasion. As the cytosolic ZNF204P shares miRNA binding sites with OCT4 and SOX2, well-known drivers of pluripotency and self-renewal, we propose that ZNF204P promotes tumorigenesis through the miRNA-145-5p/OCT4, SOX2 axis.

• Molecular & Cellular Toxicology
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• 제1권1호
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• pp.13-16
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• 2005

The current vision of toxicogenomics is the development of methods or platforms to predict toxicity of un characterized chemicals by using '-omics' information in pre-clinical stage. Because each chemical has different ADME (absorption, distribution, mechanism, excretion) and experimental animals have lots of variation, precise prediction of chemical's toxicity based on '-omics' information and toxicity data of known chemicals is very difficult problem. So, the importance of bioinformatics is more emphasized on toxicogenomics than other functional genomics studies because these problems can not be solved only with experiments. Thus, toxicoinformatics covers all information-based analytical methods from gene expression (bioinformatics) to chemical structures (cheminformatics) and it also deals with the integration of wide range of experimental data for further extensive analyses. In this review, the overall strategy to toxicoinformatics is discussed.

• Ocean and Polar Research
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• 제33권2호
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• pp.171-183
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• 2011

Despite technological developments and application advances of Acoustic Doppler Current Profilers (ADCPs), no standard procedure has been adopted or accepted for calibration of ADCPs. Limitations of existing facilities for calibrating ADCPs, the complexity of ADCP instruments, and rapid changes in ADCP technology are some of the reasons why a standard procedure has not been adopted. However, there is increasing realization of the need for effective Quality Assurance (QA) and as part of that the importance of standardized calibration. In this study, the significance of calibration and QA plans for ADCPs is discussed and the calibration facilities for ADCPs at home and abroad are reported. Furthermore, the method for calibrating ADCPs using a towed car and its limitations are discussed. This study contributes to discussions surrounding the establishment of standard procedures for calibrating ADCPs and QA plans, and the construction of calibration facilities in the future.

• IMMUNE NETWORK
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• 제14권2호
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• pp.73-80
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• 2014

Because autoimmune diseases (AIDs) result from a complex combination of genetic and epigenetic factors, as well as an altered immune response to endogenous or exogenous antigens, systems biology approaches have been widely applied. The use of multi-omics approaches, including blood transcriptomics, genomics, epigenetics, proteomics, and metabolomics, not only allow for the discovery of a number of biomarkers but also will provide new directions for further translational AIDs applications. Systems biology approaches rely on high-throughput techniques with data analysis platforms that leverage the assessment of genes, proteins, metabolites, and network analysis of complex biologic or pathways implicated in specific AID conditions. To facilitate the discovery of validated and qualified biomarkers, better-coordinated multi-omics approaches and standardized translational research, in combination with the skills of biologists, clinicians, engineers, and bioinformaticians, are required.