• Genomics & Informatics
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• v.11 no.1
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• pp.55-57
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• 2013

Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.

• Journal of Ginseng Research
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• v.45 no.2
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• pp.273-286
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• 2021

Background: Prostate carcinoma is the second most common cancer among men worldwide. Developing new therapeutic approaches and diagnostic biomarkers for prostate cancer (PC) is a significant need. The Chinese herbal medicine Panax quinquefolius saponins (PQS) have been reported to show anti-tumor effects. We hypothesized that PQS exhibits anti-cancer activity in human PC cells and we aimed to search for novel biomarkers allowing early diagnosis of PC. Methods: We used the human PC cell line DU145 and the prostate epithelial cell line PNT2 to perform cell viability assays, flow cytometric analysis of the cell cycle, and FACS-based apoptosis assays. Microarray-based gene expression analysis was used to display specific gene expression patterns and to search for novel biomarkers. Western blot and quantitative real-time PCR were performed to demonstrate the expression levels of multiple cancer-related genes. Results: Our data showed that PQS inhibited the viability of DU145 cells and induced cell cycle arrest at the G1 phase. A significant decrease in DU145 cell invasion and migration were observed after 24 h treatment by PQS. PQS up-regulated the expression levels of p21, p53, TMEM79, ACOXL, ETV5, and SPINT1 while it down-regulated the expression levels of bcl2, STAT3, FANCD2, DRD2, and TMPRSS2. Conclusion: PQS promoted cells apoptosis and inhibited the proliferation of DU145 cells, which suggests that PQS may be effective for treating PC. TMEM79 and ACOXL were expressed significantly higher in PNT2 than in DU145 cells and could be novel biomarker candidates for PC diagnosis.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.309-314
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• 2013

Aim: Brain tumors almost universally have fatal outcomes; new therapeutics are desperately needed and will only come from improved understandins of glioma biology. Methods: Exosomes are endosomally derived 30~100 nm membranous vesicles released from many cell types. Examples from GL26 cells were here purified using density gradient ultracentrifugation and monitored for effects on GL26 tumor growth in C57BL/6j mice (H-2b). Lactate dehydrogenase release assays were used to detect the cytotoxic activity of CD8+T and NK cells. Percentages of immune cells producing intracellular cytokines were analyzed by FACS. Results: In this study, exosomes from murine-derived GL26 cells significantly promoted in vivo tumor growth in GL26-bearing B6 mice. Then we further analyzed the effects of the GL26 cells-derived exosomes on immune cells including CD8+T, CD4+T and NK cells. Inhibition of CD8+T cell cytotoxic activity was demonstrated by CD8+T cell depletion assays in vivo and LDH release assays in vitro. The treatment of mice with exosomes also led to a reduction in the percentages of CD8+T cells in splenocytes as determined by FACS analysis. Key features of CD8+T cell activity were inhibited, including release of IFN-gamma and granzyme B. There were no effects of exosomes on CD4+T cells and NK cells. Conclusion: Based on our data, for the first time we demonstrated that exosomes from murine derived GL26 cells promote the tumor growth by inhibition of CD8+T cells in vivo and thus may be a potential therapeutic target.

• Food Science and Preservation
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• v.13 no.4
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• pp.495-500
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• 2006

In order to investigate whether antioxidant biomaterials inhibits IL-4 and/or IL-13 expression in vitro and in vivo, we carried out antioxidant assays by enzyme or cell-based assays with Helianthus annuus extract. Antioxidant assays include DPPH, FRAP, hydroxyl radical assays. Helianthus annuus extract exhibited SOD scavenging activity, and had different patterns by each solvent extracted reaction. DW extract inhibited oxidative stress by $H_2O_2$ that induced apoptosis. We measured $CD4^+$ cell and IL-/13 cytokine expression in a classical mouse animal model. The result show that Helianthus annuus extract showed strung inhibition of immune response in the lung. These result suggest that Helianthus annuus extract can reduce inflammation induced by n mouse asthma model.

• Ceramist
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• v.21 no.3
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• pp.204-215
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• 2018

Proteases are one of the most abundant classes of enzymes in living organisms and have been considered major targets for drug development. However, despite the ability to specifically cleave their substrates, many attempts to assay protease activity have generally relied upon the use of gel zymography or fluorophore-labeled peptide substrates, which is limited in rapid and multiplex analysis. Here we review the recent advances in nanoparticle (NP)-utilized assays of protease activity focused on in vitro and cell imaging-based approaches. Owing to large surface area and unprecedented physical properties of NPs, these approaches are anticipated to facilitate many applications related to protease activity-based disease diagnosis and drug discovery.

• Proceedings of the KSME Conference
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• 2008.11a
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• pp.1455-1457
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• 2008

Cell adhesion is a coordinated process involving initial binding of integrin receptors to extracellular matrix (ECM), recruitment of adhesion proteins, and focal adhesion assembly. The formation of mechanically stable focal adhesion assembly of cells within surrounding ECM is a key parameter to direct numerous cellular functions including cell migration, differentiation, and apotosis. With current cell adhesion assays, it is difficult to understand contributions of each coordinated event on evolution of cell adhesion strengthening since cells spontaneously spread upon their adhesion to the substrate, thus remodeling their cytoskeletal structure. In this presentation, novel approaches for analysis of cell adhesion strengthening process based on the combination of mechanical device, micro-patterned substrates, and molecular biological techniques will be discussed.

• Journal of Gastric Cancer
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• v.15 no.4
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• pp.223-230
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• 2015

Purpose: The purpose of this pilot study was to evaluate the association between adenosine triphosphate-based chemotherapy response assays (ATP-CRAs) and subsets of tumor infiltrating lymphocytes (TILs) in gastric cancer. Materials and Methods: In total, 15 gastric cancer tissue samples were obtained from gastrectomies performed between February 2007 and January 2011. Chemotherapy response assays were performed on tumor cells from these samples using 11 chemotherapeutic agents, including etoposide, doxorubicin, epirubicin, mitomycin, 5-fluorouracil (5-FU), oxaliplatin, irinotecan, docetaxel, paclitaxel, methotrexate, and cisplatin. TILs in the tissue samples were evaluated using antibodies specific for CD3, CD4, CD8, Foxp3, and Granzyme B. Results: The highest cancer cell death rates were induced by etoposide (44.8%), 5-FU (43.1%), and mitomycin (39.9%). Samples from 10 patients who were treated with 5-FU were divided into 5-FU-sensitive and -insensitive groups according to median cell death rate. No difference was observed in survival between the two groups (P=0.216). Only two patients were treated with a chemotherapeutic agent determined by an ATP-CRA and there was no significant difference in overall survival compared with that of patients treated with their physician's choice of chemotherapeutic agent (P=0.105). However, a high number of CD3 TILs was a favorable prognostic factor (P=0.008). Pearson's correlation analyses showed no association between cancer cell death rates in response to chemotherapeutic agents and subsets of TILs. Conclusions: Cancer cell death rates in response to specific chemotherapeutic agents were not significantly associated with the distribution of TIL subsets.

• Journal of the Optical Society of Korea
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• v.16 no.1
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• pp.42-46
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• 2012

We have developed a fluorescence optical detection system using a digital micromirror device (DMD) for monitoring 3D cell culture matrices in situ. Full 3D imaging with fast scanning speed was implemented by the combined action of a DMD and a motorized stage. Imaging results with fluorescent microbeads measure the minimum axial resolution of the system as $6.3{\mu}m$, while full 1-mm scanning through 3D alginate-based matrix was demonstrated. For cell imaging, improved images were obtained by removing background fluorescence although the scanning distance was reduced because of low intracellular fluorescence efficiency. The system is expected to be useful to study various dynamics and behaviors of 3-dimensionally cultured cells in microfluidic systems.

• International Journal of Stem Cells
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• v.17 no.2
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• pp.182-193
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• 2024

To address the limitations of animal testing, scientific research is increasingly focused on developing alternative testing methods. These alternative tests utilize cells or tissues derived from animals or humans for in vitro testing, as well as artificial tissues and organoids. In western countries, animal testing for cosmetics has been banned, leading to the adoption of artificial skin for toxicity evaluation, such as skin corrosion and irritation assessments. Standard guidelines for skin organoid technology becomes necessary to ensure consistent data and evaluation in replacing animal testing with in vitro methods. These guidelines encompass aspects such as cell sourcing, culture techniques, quality requirements and assessment, storage and preservation, and organoid-based assays.

• Fisheries and Aquatic Sciences
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• v.7 no.3
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• pp.122-129
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• 2004

Harmful Cochlodinium polykrikoides is a notorious harmful algal bloom (HAB) species that is causing mass mortality of farmed fish along the Korean coast with increasing frequency. We analyzed the sequence of the large subunit (LSD) rDNA D1-D3 region of C. polykrikoides and conducted phylogenetic analyses using Bayesian inference of phylogeny and the maximum likelihood method. The molecular phylogeny showed that C. polykrikoides had the genetic relationship to Amphidinium and Gymnodinium species supported only by the relatively high posterior probabilities of Bayesian inference. Based on the LSU rDNA sequence data of diverse dinoflagellate taxa, we designed the C. polykrikoides-specific PCR primer set, CPOLY01 and CPOLY02 and developed PCR detection assays for its sensitive, accurate HAB monitoring. CPOLY01 and CPOLY02 specifically amplified C. polykrikoides and did not cross-react with any dinoflagellates tested in this study or environmental water samples. The effective annealing temperature $(T_{p})$ of CPOLY01 and CPOLY02 was $67^{\circ}C$. At this temperature, the conventional and nested PCR assays were sensitive over a wide range of C. polykrikoides cell numbers with detection limits of 0.05 and 0.0001 cells/reaction, respectively.