• BMB Reports
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• v.47 no.11
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• pp.619-624
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• 2014

Antisense RNA is a type of noncoding RNA (ncRNA) that binds to complementary mRNA sequences and induces gene repression by inhibiting translation or degrading mRNA. Recently, several small ncRNAs (sRNAs) have been identified in Escherichia coli that act as antisense RNA mainly via base pairing with mRNA. The base pairing predominantly leads to gene repression, and in some cases, gene activation. In the current study, we examined how the location of target sites affects sRNA-mediated gene regulation. An efficient antisense RNA expression system was developed, and the effects of antisense RNAs on various target sites in a model mRNA were examined. The target sites of antisense RNAs suppressing gene expression were identified, not only in the translation initiation region (TIR) of mRNA, but also at the junction between the coding region and 3' untranslated region. Surprisingly, an antisense RNA recognizing the upstream region of TIR enhanced gene expression through increasing mRNA stability.

• The Journal of Korean Medicine
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• v.29 no.3
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• pp.76-87
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• 2008

Objectives: In this study, the author investigated whether Haengso-tang (HST) and Chwiyeon-tang (CHT) affect both in vitro mucin secretion and MUC5AC gene expression in airway epithelial cells and in vivo mucin secretion from animal model for airway mucus hypersecretion. Materials and Methods: Confluent HTSE cells (non-labeled) were chased for 30 min in the presence of HST and CHT to assess the effects of the agents on mucin secretion by enzyme-linked immunosorbent assay (ELISA), with removal of oriental herbal medicine extract from each agent-treated sample by centrifuge microfilter. Also, the effects of the agents on TNF- or EGF-induced MUC5AC gene expression in human airway epithelial cells (NCI-H292) were investigated. The author also induced hypersecretion of airway mucus by exposure of rats to SO2 for 3 weeks. Effects of orally-administered HST and CHT during 1 week on in vivo mucin secretion from tracheal goblet cells of rats were assessed using ELISA. Results: (1) HST significantly decreased in vitro mucin secretion from cultured HTSE cells. However, CHT did not affect in vitro mucin secretion from HTSE cells; (2) CHT significantly inhibited the expression levels of EGF- or TNF-alpha-induced MUC5AC gene in NCI-H292 cells. However, HST did not affect the expression levels of EGF- or TNF-alpha-induced MUC5AC gene in NCI-H292 cells; (3) CHT significantly inhibited hypersecretion of in vivo mucin. However, HST did not affect hypersecretion of in vivo mucin. Conclusion: These results suggest that CHT can not only affect the secretion of mucin but also the expression of the mucin gene and could be helpful for treating pulmonary disease caused by secretion of mucin.

• Proceedings of the Botanical Society of Korea Conference
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• 1987.07a
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• pp.349-356
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• 1987

Insertions of transposable elements in or near a structural gene give rise to null phenotypes, reduced levels of gene expression, or alteration on the tissue-specific pattern of gene expression. Null phenotypes often result from insertions in exons. Reduced levels of gene expression results from insertions in various regions such as promoter region, 5' non-translated region, exon and intron. The maize allele of Adh1-3F1124 is an example of alteration in the tissue-specific patetern of gene expression. Adh1-3F1124 contains a Mu element inserted 31 bp 5' to the transcriptional start site of the wild-type Adh1 activity in seeds and anaerobically-treated seedlings but normal levels in the pollen. Upon the insertion of a transposable element a certain number of host DNA sequences at the insertion site is duplcated. When transposable elements excise, all element sequences are deleted. However, the duplicated host sequences may be left intact or deleted to various extents. This results in null phenotypes, restoration of original levels of gene expression, or altered levels of gene expression. On the basis of effects of transposable-element insertions or excisions on gene expression, the usefulness of transposable ellements for studies on gene expression is discussed.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.12
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• pp.4897-4902
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• 2014

Purpose: To investigate the anticancer effects and underlying mechanisms of parthenolide on HepG2 human hepatocellular carcinoma cells. Materials and Methods: Cell viability was assessed by MTT assay and cell apoptosis through DAPI, TUNEL staining and Western blotting. Monodansylcadaverin(MDC) and AO staining were used to detect cell autophagy. Cell proliferation was assessed by Ki67 immunofluorescence staining. Results: Parthenolide induced growth inhibition in HepG2 cells. DAPI and TUNEL staining showed that parthenolide could increase the number of apoptotic nuclei, while reducing the expression of the anti-apoptotic protein Bcl-2 and elevating the expression of related proteins, like p53, Bax, cleaved caspase9 and cleaved caspase3. Parthenolide could induce autophagy in HepG2 cells and inhibited the expression of proliferation-related gene, Ki-67. Conclusions: Parthenolide can exert anti-cancer effects by inducing cell apoptosis, activating autophagy and inhibiting cell proliferation.

• KSBB Journal
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• v.13 no.4
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• pp.418-423
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• 1998

Cellular transfections with cationic liposomes are widely empolyed for gene and oligonucleotide transfer in vitro because of their safety and ease of use. However, they still suffer from the low transfection efficiency comparing with viral vectors. Substantial effort shave been focused on increasing transfection efficiency by supplementing the liposome/DNA complexes(lipoplex) with various components. In this work, we tired three kinds of supplements, Poly-L-lysine(PLL), transferrin and a mixture of anionic lipids(PS/PE/PC), to study their effects on gene transfer yield and gene expression efficiency. PLL, a polycationic polymer, enhanced gene transfer yield by 3 times but the gene expression efficiency was increased only by 1.5 times. this result implies that PLL can enhance the transfection efficiency mainly by increasing the rate of outermembrane transport of lipoplex into the cells. On the other hand, transferrin which can facilitate the gene transfer via ligand-receptor interaction gave not only increased gene transfer yield but also enhanced gen expression efficiency by 2.8 times. Transferrin seems to contribute to the escape of plasmid from endosomes through ligand-receptor recycle mechanism. When the cells were treated with a mixture of anionic lipids for 3 hours before the transfection, gene transfer yield was slightly decreased but the gene expression efficiency was enhanced by 1.9 times. This is presumably due to the accelerated liposome-plasmid dissociation by the anionic lipids, and the increased delivery of plasmid to the nucleus. According to these results, it is clear that the supplementation to ameliorate transfection efficiency with cationic liposomes should be contrived in the direction of increasing delivery of plasmid.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.42 no.5
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• pp.626-631
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• 1997

This study was conducted to clarify the genetic effect on the duration of grain filling with using the eight corn inbreds. In diallel cross analysis, the grain filling during the lag period showed partial dominance with great additive effects. Inbreds FR14A and A508 showed greater recessive gene effects for lag period, while FR25 showed greater effects of dominant genes. The genetic analysis for the effective filling period(EFP) showed over dominance without additive gene effects. FR25 of 8 inbreds showed greatest effects of dominant genes for EFP, while YUBC208 showed greater recessive gene effects for EFP than other inbreds. The genetic analysis for total grain filling period(TGFP) seemed to be due to partial dominance with greater additive effects. Early inbred line, YUBC208 especially showed greater recessive gene effects for TGFP than others. No. of effective genes related to EFP and TGFP were estimated by at least 5.

• Genomics & Informatics
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• v.14 no.4
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• pp.160-165
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• 2016

Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide polymorphisms. However, such tests are computationally demanding and methodologically challenging. Recently, a simple but powerful method, named "BOolean Operation-based Screening and Testing" (BOOST), was proposed for genome-wide gene-gene interaction analyses. BOOST was designed with a Boolean representation of genotype data and is approximately equivalent to the log-linear model. It is extremely fast, and genome-wide gene-gene interaction analyses can be completed within a few hours. However, BOOST can not adjust for covariate effects, and its type-1 error control is not correct. Thus, we considered two-step approaches for gene-gene interaction analyses. First, we selected gene-gene interactions with BOOST and applied logistic regression with covariate adjustments to select gene-gene interactions. We applied the two-step approach to type 2 diabetes (T2D) in the Korea Association Resource (KARE) cohort and identified some promising pairs of single-nucleotide polymorphisms associated with T2D.

• Journal of Periodontal and Implant Science
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• v.42 no.3
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• pp.95-104
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• 2012

Purpose: The purpose of this study was to determine whether increasing the Ti6Al4V surface oxide negative charge through heat ($600^{\circ}C$) or radiofrequency plasma glow discharge (RFGD) pretreatment, with or without a subsequent coating with fibronectin, stimulated osteoblast gene marker expression in the MC3T3 osteoprogenitor cell line. Methods: Quantitative real-time polymerase chain reaction was used to measure changes over time in the mRNA levels for osteoblast gene markers, including alkaline phosphatase, bone sialoprotein, collagen type I (${\alpha}1$), osteocalcin, osteopontin and parathyroid hormone-related peptide (PTH-rP), and the osteoblast precursor genes Runx2 and osterix. Results: Osteoprogenitors began to differentiate earlier on disks that were pretreated with heat or RFGD. The pretreatments increased gene marker expression in the absence of a fibronectin coating. However, pretreatments increased osteoblast gene expression for fibronectin-coated disks more than uncoated disks, suggesting a surface oxide-mediated specific enhancement of fibronectin's bioactivity. Heat pretreatment had greater effects on the mRNA expression of genes for PTH-rP, alkaline phosphatase and osteocalcin while RFGD pretreatment had greater effects on osteopontin and bone sialoprotein gene expression. Conclusions: The results suggest that heat and RFGD pretreatments of the Ti6Al4V surface oxide stimulated osteoblast differentiation through an enhancement of (a) coated fibronectin's bioactivity and (b) the bioactivities of other serum or matrix proteins. The quantitative differences in the effects of the two pretreatments on osteoblast gene marker expression may have arisen from the unique physico-chemical characteristics of each resultant oxide surface. Therefore, engineering the Ti6Al4V surface oxide to become more negatively charged can be used to accelerate osteoblast differentiation through fibronectin-dependent and independent mechanisms.

• The Journal of Korean Medicine
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• v.27 no.1 s.65
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• pp.11-22
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• 2006

Objectives : In this study, the aim was to investigate the inhibitory effects of Bangpungtong-seoung-san on the obese gene and obese inhibitory about obese-mouse induced by high fat diet. Methods : In order to investigate the effects of Bangpuangtongseoung-san(BPTS) on the obese gene and obese inhibitory, C57BL/6 mice were induced by high fat diet. C57BL/6 mice were divided into three groups(normal, high fat diet with control, high fat diet with BPTS extract) and fed for 13weeks. Results : 1. The change of body weight and the final increase of body weight were decreased significantly. 2. The amount of the adipocyte in body weight was decreased significantly. 3. In primary adipocytes, ${\beta}3AR$ gene expression was increased significantly and leptin gene expression was decreased in $100{\mu}g/ml$ density significantly. 4. In primary adipocytes, the amount of TNF-${\alpha}$ was decreased in $100{\mu}g/ml$ density significantly and the amount of leptin was decreased but did not show significance. 5. In adipocytes tissue, the expression of leptin was decreased and the expression of ${\beta}3AR$ was increased. Conclusions : These results suggest that BPTS may inhibit the expression of the obese gene mad obese inhibitory about obese-mouse induced by high fat diet.

• Molecules and Cells
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• v.42 no.8
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• pp.579-588
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• 2019

Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. GSEA may be suboptimal for functional gene sets; however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. We also repurposed FDA-approved drugs using NGSEA and experimentally validated budesonide as a chemical with anti-cancer effects for colorectal cancer. We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. NGSEA is freely available at www.inetbio.org/ngsea.