• Genomics & Informatics
• /
• v.18 no.4
• /
• pp.46.1-46.4
• /
• 2020

We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.

• The Korea Journal of Herbology
• /
• v.31 no.2
• /
• pp.13-19
• /
• 2016

Objectives : The present study was designed to evaluate the protective effect of Allium tuberosum (AT) extract on atherosclerosis in LDL receptor knockout (LDLr KO) mouse fed western diet.Methods : The AT was extracted 70% ethanol. The experimental groups were divided with four groups of LDLr KO mice, one group fed a normal diet and the others fed a Western diets for 8weeks. Two Western diet groups were orally administered AT extract at dosage of 100 and 300 mg/kg body weight. The body weight and food intake were measured every day. We measured levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), triglyceride (TG), total cholesterol (TC), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and Glucose in serum. Also, effect of AT extract performed using H&E staining.Results : The AT treatment groups showed decrease in body weight and food efficiency in comparison with control group. Blood biochemistry parameters such as TG, TC, LDL, and glucose levels were increased in control group, while AT treatment groups were reduced. Also, the increased levels of ALT and AST were improved by AT extract. We confirmed that the weights of liver, kidney, subcutaneous fat, epididymal fat, kidney leaf fat, and intraabdominal fat were change in LDLr KO mice treated AT extract. In addition, histopathological changes in liver and aorta were similar to normal group.Conclusions : Based on these results, the AT extract is considered to make prevention of atherosclerosis through reduction and functional improvement of the liver and vascular endothelial cells in the body fat accumulation and lipid content in LDLr ko mouse model.

• Proceedings of the Korean Society of Toxicology Conference
• /
• 1998.10a
• /
• pp.8-13
• /
• 1998

Polyoma Virus Enhancer core Binding Protein (PEBP2)는 유전자의 전사를 조절하는 hetero-dimeric transcription factor로서 $\alpha$와 $\beta$ subunit으로 구성되어 있다. $\alpha$ subunit을 coding 하는 유전자중 하나인 PEBP2aB는 급성백혈병과 관련되어있는 t(8;21) 또는 t(12;21)에 의하여 변형됨으로서 백혈병 발병의 원인이 되고 있다 (Miyoshi et al., 1993; .Romana et al., 1995). $\beta$ subunit을 coding 하는 PEBP2$\beta$도 inv(16)에 의하여 변형됨으로서 백혈병을 유도하는 주요 원인이 되고 있다 (Liu et al., 1993). 이 유전자들의 생물학적 활성을 밝히기 위한 연구가 gene targeting에 의한 knockout mouse 생산 방법으로 수행되었다. 그 결과 PEBP2$\alpha$B와 PEBP2$\beta$ 유전자가 definitive hematopoiesis에 있어서 결정적으로 중요한 역할을 하고 있음이 관찰되었다 (Okuda et al., 1996, Wang et al., 1996a, 1996b), 이는 이들 유전자가 bematopoietic master switch 유전자임을 밝힌 중요한 결과로서 이로부터 혈액학 연구 분야의 새로운 장이 열리게 되었다. 또한 이러한 연구 결과들은 PEBP2 family에 속하는 다른 유전자의 생물학적 활성의 연구를 촉진하는 계기가 되었다. 최근 PEBP2$\alpha$A 유전자가 결손된 마우스가 생산되었는데 이 유전자의 경우에는 모든 종류의 뼈의 생성이 완전히 결손됨이 관찰되었다 (Komori et al., 1997). 이는 PEBP2$\alpha$A 유전자가 뼈의 생성을 지배하는 master switch 유전자임을 보여주는 중요한 관찰로서 bone biologist 들의 큰 관심을 모으고 있다. 본 연구팀은 PEBP2 family 유전자 중 유일하게 아직 생물학적 활성이 규명되지 않은 PEBP2$\alpha$C 유전자의 활성을 knockout 마우스를 생산하는 방법에 의하여 분석하였으며 소화기관의 형성에 중요한 역할을 하고 있음을 확인하였다.

• The Korean Journal of Physiology and Pharmacology
• /
• v.24 no.3
• /
• pp.233-240
• /
• 2020

Autophagy regulators are often effective as potential cancer therapeutic agents. Here, we investigated paclitaxel sensitivity in cells with knockout (KO) of ATG5 gene. The ATG5 KO in multidrug resistant v-Ha-ras-transformed NIH 3T3 cells (Ras-NIH 3T3/Mdr) was generated using the CRISPR/Cas9 technology. The qPCR and LC3 immunoblot confirmed knockout of the gene and protein of ATG5, respectively. The ATG5 KO restored the sensitivity of Ras-NIH 3T3/Mdr cells to paclitaxel. Interestingly, ATG5 overexpression restored autophagy function in ATG5 KO cells, but failed to rescue paclitaxel resistance. These results raise the possibility that low level of resistance to paclitaxel in ATG5 KO cells may be related to other roles of ATG5 independent of its function in autophagy. The ATG5 KO significantly induced a G₂/M arrest in cell cycle progression. Additionally, ATG5 KO caused necrosis of a high proportion of cells after paclitaxel treatment. These data suggest that the difference in sensitivity to paclitaxel between ATG5 KO and their parental MDR cells may result from the disparity in the proportions of necrotic cells in both populations. Thus, our results demonstrate that the ATG5 KO in paclitaxel resistant cells leads to a marked G₂/M arrest and sensitizes cells to paclitaxel-induced necrosis.

• The Korea Journal of Herbology
• /
• v.31 no.1
• /
• pp.17-23
• /
• 2016

Objectives : This study was designed to protect effect on atherosclerosis through regulation of low density lipoprotein(LDL) by 70 % ethanol extract Ganoderma lucidum (GL) in LDL receptor knockout mouse (LDLr ko mice) fed Western diet.Methods : The LDLr ko mice were divided into 3 groups ; Control, GL100, and GL300. After grouping, LDLr ko mice were fed Western diet. The GL (100 or 300 mg/kg body weight/day, p.o.) was administered every day for 8 weeks. The body weight and food intake were measured every day. The changes in the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatinine, triglyceride (TG), total cholesterol (TC), and high-density lipoprotein (HDL) in serum were analyzed after experiment.Results : The LDLr ko mice fed Western diet were increased body weight gain and blood biochemistry parameters such as ALT, AST, TG, TC, and LDL. However GL300 group significantly reduced the body weight. Also TG, TC, and LDL level did not increase. The levels of ALT, AST, HDL were not changed. Also, LDLr ko mice model liver were observed lipid drop, but GL groups did not appear. Futhermore, histological analysis of GL groups aorta tissue were similar to NOR groups.Conclusions : We confirmed that whether GL administration is protect atherosclerosis or not. As the results, blood biochemistry and histological analysis did not changed much in GL administration groups. This study provides scientific evidence that GL protect the atherosclerosis through the reduction of LDL cholesterol. Therefore GL has potential medicine inhibition of atherosclerosis.

• Journal of Korean Dental Science
• /
• v.9 no.1
• /
• pp.9-18
• /
• 2016

Purpose: Wnt signaling plays an essential role in the dental epithelium and mesenchyme during tooth morphogenesis. Deletion of the Wntless (Wls) gene in odontoblasts appears to reduce canonical Wnt activity, leading to inhibition of odontoblast maturation. However, it remains unclear if autonomous Wnt ligands are necessary for differentiation of dental pulp cells into odontoblast-like cells to induce reparative dentinogenesis, one of well-known feature of pulp repair to form tertiary dentin. Materials and Methods: To analyze the autonomous role of Wls for differentiation of dental pulp cells into odontoblast-like cells, we used primary dental pulp cells from unerupted molars of Wls-floxed allele mouse after infection with adenovirus for Cre recombinase expression to knockout the floxed Wls gene or control GFP expression. The differentiation of dental pulp cells into odontoblast-like cells was analyzed by quantitative real-time polymerase chain reaction. Result: Proliferation rate was significantly decreased in dental pulp cells with Cre expression for Wls knockout. The expression levels of Osterix (Osx), runt-related transcription factor 2 (Runx2), and nuclear factor I-C (Nfic) were all significantly decreased by 0.3-fold, 0.2-fold, and 0.3-fold respectively in dental pulp cells with Wls knockout. In addition, the expression levels of Bsp, Col1a1, Opn, and Alpl were significantly decreased by 0.7-fold, 0.3-fold, 0.8-fold, and 0.6-fold respectively in dental pulp cells with Wls knockout. Conclusion: Wnt ligands produced autonomously are necessary for proper proliferation and odontoblastic differentiation of mouse dental pulp cells toward further tertiary dentinogenesis.

• The Journal of Korean Institute of Communications and Information Sciences
• /
• v.26 no.11C
• /
• pp.113-122
• /
• 2001

Several guidelines can be developed for a satellite-based ATM switch. One of the most important of these is that the switch must provide a requirement for CLRs on the order of 10-10 to meet the QoS of high- performance traffic and avoid costly retransmissions. In this paper, the proposed approach shows not only the better traffic performance but also requires the little switching elements and buffers compared with original Knockout switch and other scheduling algorithm. As a result, the complexity becomes reduced. Simulation results indicate that proposed approach shows excellent cell loss ratio compared with existing switch architecture. Also, iii performance can be approached to the cell loss ratio, which is requirement for the satellite system, as window size increases. An(1 it shows thats low complexity is induced. Therefore, the proposed approach is appropriate for satellite on-board ATM switch architecture.

• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.7
• /
• pp.1029-1036
• /
• 2017

Objective: In the livestock industry, the regulatory mechanisms of muscle proliferation and differentiation can be applied to improve traits such as growth and meat production. We investigated the regulatory pathway of MyoD and its role in muscle differentiation in quail myoblast cells. Methods: The MyoD gene was mutated by the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technology and single cell-derived MyoD mutant sublines were identified to investigate the global regulatory mechanism responsible for muscle differentiation. Results: The mutation efficiency was 73.3% in the mixed population, and from this population we were able to establish two QM7 MyoD knockout subline (MyoD KO QM7#4) through single cell pick-up and expansion. In the undifferentiated condition, paired box 7 expression in MyoD KO QM7#4 cells was not significantly different from regular QM7 (rQM7) cells. During differentiation, however, myotube formation was dramatically repressed in MyoD KO QM7#4 cells. Moreover, myogenic differentiation-specific transcripts and proteins were not expressed in MyoD KO QM7#4 cells even after an extended differentiation period. These results indicate that MyoD is critical for muscle differentiation. Furthermore, we analyzed the global regulatory interactions by RNA sequencing during muscle differentiation. Conclusion: With CRISPR/Cas9-mediated genomic editing, single cell-derived sublines with a specific knockout gene can be adapted to various aspects of basic research as well as in functional genomics studies.

• Journal of the Korea Society of Computer and Information
• /
• v.11 no.1 s.39
• /
• pp.157-165
• /
• 2006

This paper proposes a new output-buffered multicast ATM switch with tandem crosspoints switching fabric, named the MTCOS(Multicast Tandem Crosspoint Output-buffered Switch). The MTCOS consists of multiple simple crosspoint switch fabrics, named TCSF(Tandem Crosspoint Switch Fabric) , and concentrated output buffers for efficient multicasting. The TCSF resolves the cell delay deviation problem which the self-routing crossbar switches inherently have. Further, it offers multiple concurrent pathes from one input to multiple output ports. It also provides multi-channel switching by easy software configuration and has several desirable characteristics such as scalability, high Performance, and modularity. A shared traffic concentration and output queuing strategies of the MTCOS results in lower cell loss as well as lower cell delay time over a wide range of multicast traffic. Furthermore, it has lower hardware complexity than that of the SCOQ and Knockout multicast switch to achieve the same Knockout concentration rate as the conventional switches. It is shown that the proposed switch can be easily applied to design high performance for any multicast traffic by analytic analysis and computer simulation.

• Toxicological Research
• /
• v.17
• /
• pp.299-304
• /
• 2001

Xenobiotics and their reactive intermediates bind to cellular macromolecules and/or generate oxidative stress. which provoke deleterious effects on the cell function. Induction of xenobiotic-biotrans-forming enzymes and antioxidant molecules is an important defense mechanism against such insults. A group of genes involved in the defense mechanism. e.g. genes encoding glutathione S-transferases. NAD(P)H: quinone oxidoreductase, UDP-glucuronosyltransferase (UDP-GT) and ${\gamma}$-glutamylcysteine synthetase (GGCS). have a common regulatory sequence, Antioxidant or Electrophile Responsive Element (ARE/EpRE). Recently. Nrf2. discovered as a homologue of erythroid transcription factor p45 NF-E2, was shown to bind ARE/EpRE and induce the expression of these defense genes. Mice that lack Nrf2 show low basal levels of expression and/or impaired induction of these genes. which makes the animals highly sensitive to xenobiotic toxicity. Indeed. we show here that nrf2-deficient mice had a higher mortality than did the wild-type mice when exposed to acetaminophen (APAP). Detailed analyses of APAP hepatotoxicity in the nrf2 knockout mice indicate that a large amount of reactive APAP metabolites was generated in the livers due to the impaired basal expression of two detoxifying enzyme genes, UDP-GT (Ugt1a6) and GGCS. while the cytochrome P450 content was unchanged. Thus. the studies using the nrf2 knockout mice clearly demonstrate significance of the expression of Nrf2-regulated enzymes in protection against xenobiotic toxicity.