• The Korean Journal of Applied Statistics
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• v.35 no.5
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• pp.667-684
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• 2022

Gene expression data present the level of mRNA abundance of each gene, and analyses of gene expressions have provided key ideas for understanding the mechanism of diseases and developing new drugs and therapies. Nowadays high-throughput technologies such as DNA microarray and RNA-sequencing enabled the simultaneous measurement of thousands of gene expressions, giving rise to a characteristic of gene expression data known as high dimensionality. Due to the high-dimensionality, learning models to analyze gene expression data are prone to overfitting problems, and to solve this issue, dimension reduction or feature selection techniques are commonly used as a preprocessing step. In particular, we can remove irrelevant and redundant genes and identify important genes using gene selection methods in the preprocessing step. Various gene selection methods have been developed in the context of machine learning so far. In this paper, we intensively review recent works on gene selection methods using machine learning approaches. In addition, the underlying difficulties with current gene selection methods as well as future research directions are discussed.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.89-89
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• 2003

본 연구에서는 1.7kb 및 3.1kb bovine $\beta$-casein promoter의 유전자 발현 조절능력을 알아보기 위해 1 7kb 및 3.1kb bovine $\beta$-casein promoter에 human Type II Collagen 유전자를 연결해서 DNA microinjection으로 형질전환생쥐를 생산하였다. 총 8마리의 founder생쥐(1.7kb collagen : 5마리, 3.1kb collagen 3마리)를 생산하였고 이 founder생쥐와 wild type 생쥐를 mating시켜서 $F_1 및 F_2$ 새끼를 얻었다. $F_1 및 F_2$새끼들에서 human Type II collagen 유전자의 transmission rate는 약 50%로 Mendel의 법칙에 따라 분리되어 안정적으로 유전자가 염색체에 정착되어 있음을 확인하였다. 이들 $F_1 및 F_2$새끼 중 암컷들을 임신시켜 분만 후 5-10 일경에 유선조직을 포함하여 여러 조직으로부터 RNA를 추출하여 Northern blotting 및 RT-PCR 방법을 이용하여 Type II collagen mRNA의 발현을 분석하였다. 유선에서의 발현은 1 7 kb 및 3.1 kb line별로 각각 1 line씩 발현되지 않았고, 그 외 line에서는 모두 발현되는 것으로 확인되었다. 유선에서의 Type II collagen mRNA 발형양은 1.7 kb 및 3.1 kb bovine $\beta$-casein promoter사이에서는 큰 차이를 나타내지 않았으나 1.7 kb promoter 형질전환생쥐의 경우 유선 이외 조직에서도 발현되는 양상을 나타내었고, 3.1kb promoter line에서는 유선특이적으로 발현시키는 양상을 나타내었다. 그러므로 bovine $\beta$-casein promoter의 1.7 kb와 3.1 kb 사이에 유선특이적 발현을 유도하는 조절부위가 있을 것으로 추정된다.

• Korean Journal of Microbiology
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• v.22 no.4
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• pp.235-242
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• 1984

Sep gene, which is one of the cell division genes coding for penicillin binding protein 3 was subcloned from ${\lambda}607sep^{+2}$ to plasmid pBR322. which has a strong promotor such as lac UV5(lacP). It was confirmed that the sep gene cloned to pLJ3 was in the proper orientation for expressionfrom lactose promotor. To analyze the expression efficiency of sep gene within the plasmids newly constructed, sep mRNA was assated by using ${\lambda$\mid$\;607sep^{+2}$ DNA as a probe. Sep mRNA level was increased 25 times in the cells carrying sep gene cloned to pBR322 compared to E. coli C600 which has wild type sep gene within the chromosome instead of plasmed. Furthermore, the cells carrying sep gene cloned to pLJ3 derected the synthesis of about 50 times as much sep mRNA as did cells carrying sep gene cloned to pBR 322, representing that the sep gene was successfully cloned to pLJ3.

• Journal of the Korean Society of Food Science and Nutrition
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• v.34 no.5
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• pp.573-580
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• 2005

Cholesterol $7\alpha-hydroxylase$ (CYP7A1) is the rate-limiting enzyme in the conversion of cholesterol to bile acids and plays a central role in regulating cholesterol homeostasis. We previously showed that a fermentable $\beta-glucan$ ingestion decreased plasma cholesterol levels due to fecal bile acid excretion elevation involved inincrease of cholesterol $7\alpha-hydroxylase$ mRNA expression and activity. It is proposed that short chain fatty acids (SCFA) produced by cecal and colonic fermentation of soluble fiber are associated with cholesterol-lowering effect of fiber. In the present study, we investigated whether CYP7A1 expression is up-regulated by short chain fatty acids or by hormones in cultured human hepatoma (HepG2) cells. Confluent HepG2 cell were incubated with acetate, propionate, or butyrate at 1 mM concentration for 24 hrs. Acetate as well as propionate increased to 1.8-fold expression of CYP7A1 mRNA than the control. Butyrate also increased 1.5-fold expression of CYP7A1 mRNA. Our data show for the first time that SCFA increase expression of CYP7A1 mRNA. Adding insulin, dexamethasone and triiodothyronine $(1\;{\mu}M)$ to HepG2 cell increased the expression of CYP7A1 mRNA to $150\%,\;173\%,\;141\%$, respectively. These results suggest that SCFA produced by cecal fermentation stimulate enteric nervous system, in which secreted some neuropeptides may be responsible for change in cholesterol and bile acid metabolism. These findings suggest that SCFA are involved in lowering plasma cholesterol levels due to the up-regulation of CYP7A1 and bile acid synthesis.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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• v.31 no.2
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• pp.11-23
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• 2018

목적 : 본 연구에서는 $TNF-{\alpha}$와 $IFN-{\gamma}$로 자극한 인간피부각질형성세포 (HaCaT keratinocytes) 모델을 사용하여 지모가 피부장벽 기능에 미치는 영향을 알아보고자 하였다. 방법 : MTT assay를 통하여 지모 주정(70% 에탄올) 추출물 (EAA)이 HaCaT keratinocytes의 세포생존율에 미치는 영향을 확인하였으며 wound healing assay를 통해 EAA가 HaCaT 세포의 이주 능력에 영향을 주는지 관찰하였다. 또한 western blot analysis와 qRT-PCR을 통하여 EAA가 $TNF-{\alpha}/IFN-{\gamma}$로 자극한 HaCaT 세포에서 iNOS의 단백질 발현 및 IL-4, IL-13, IL-6의 mRNA 발현, filaggrin의 단백질과 mRNA 발현에 미치는 영향을 조사하였다. 결과 : EAA는 처리 농도 $500{\mu}g/ml$까지 HaCaT keratinocytes의 세포생존율에 영향을 미치지 않았다. EAA는 wound healing assay에서 HaCaT 세포의 이주 능력을 증가시켰으며, $TNF-{\alpha}/IFN-{\gamma}$로 자극한 HaCaT 세포에서 iNOS의 단백질 수준을 감소시켰다. 또한 EAA가 IL-4, IL-13, IL-6의 mRNA 발현을 억제하는 것 역시 확인할 수 있었다. 뿐만 아니라 EAA는 $TNF-{\alpha}/IFN-{\gamma}$ 자극에 의해 감소했던 filaggrin을 단백질과 mRNA 수준에서 회복시켰다. 결론 : EAA가 HaCaT 세포에서 Th2 type cytokines, pro-inflammatory cytokine의 억제와 filaggrin 회복을 통해 피부장벽 기능 손상에 대한 억제활성을 갖는 것을 확인하였으며, 이를 통해 EAA가 염증으로 인해 손상된 피부장벽 기능 개선에 효과적일 것으로 사료된다.

• Journal of Life Science
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• v.20 no.12
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• pp.1784-1791
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• 2010

In this study, we investigated the effects of ethyl alcohol extracts of Hizikia fusiforme (EHF) on the correlation between tightening of tight junctions (TJs) and anti-invasive activity in human gastric adenocarcinoma AGS cells. Inhibitory effects of EHF on cell proliferation, motility, and invasiveness were found to be associated with increased tightness of the TJs, which was demonstrated by an increase in transepithelial electrical resistance. Activities of matrix metalloprotease (MMP)-2 and -9 in AGS cells were dose-dependently inhibited by treatment with EHF, and this was also correlated with a decrease in expression of their mRNA and proteins; however, tissue inhibitor of metalloproteinase (TIMP)-1 and -2 mRNA levels were increased. Additionally, immunoblotting results indicated that EHF repressed the levels of claudin proteins (claudin-1, -3, and -4), major components of TJs that play key roles in control and selectivity of paracellular transport. Furthermore, EHF decreased expression of insulin such as growth factor-1 receptor proteins, while concurrently increasing that of thrombospondin-1 and E-cadherin. In conclusion, these results suggest that EHF treatment may inhibit tumor cell motility and invasion, and therefore act as a dietary source to decrease the risk of cancer metastasis.

• Korean Journal of Acupuncture
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• v.20 no.2
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• pp.47-54
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• 2003

목적 : 본 연구는 염증유발 내독소인 LPS 자극을 통한 면역 스트레스에 대한 약침의 치료효과와 기전을 알아보기 위해 설계되었다. LPS를 통한 염증반응은 다양한 기전을 통해 이루어지는 데 특히, 산화질소(NO)를 생성하는 효소인 iNOS의 활성은 시상하부에서 NO의 생성을 촉진함으로써 염증반응을 발현시키는 중요한 역할을 하는데 약침이 LPS로 인해 활성화된 iNOS의 발현에 어떠한 영향을 미치는지 알아보고자 하였다. 실험방법 : 흰쥐에 LPS를 투여하고 2시간 경과한 후 약침 (소염방, 대한약침학회)을 경혈 (합곡, 족삼리)에 좌,우 각각 0.2cc 씩 피하 투여하고 RT-PCR 방법을 통하여 면역활성에 중요한 역할을 하는 시상하부에서의 iNOS의 mRNA 발현을 알아 보았다. 실험결과 : LPS 투여로 인하여 증가하였던 iNOS mRNA가 약침치료를 통해 현저하게 감소하였다. 그러나 비경혈점 (미추부위 임의혈)에 약침을 투여한 군 경혈점에 생리식염수를 투여한 군에서는 iNOS mRNA 가 감소하지 않았다. 이는 약침이 LPS를 투여한 흰쥐의 시상하부에서 iNOS의 mRNA 발현에 조절작용을 가지고 있는 것을 보여주는 결과로 약침이 면역활성에 중요한 역할을 하는 NO의 생성을 억제함으로써 면역 스트레스에 치료효과를 나타내는 것으로 보여진다. 결론 : 본 연구는 약침치료가 면역반응의 중추기관인 시상하부에서 면역반응의 중요한 조절인자인 NO의 생성을 조절하는 기전을 통해 그 치료효과를 나타내는 것을 밝혔고 더 나아가 약침에 대한 현대과학적 연구에 중요한 발판을 마련했다는 점에서 그 의의를 가지고 있다고 사료된다.

• Journal of the Korean Applied Science and Technology
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• v.37 no.3
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• pp.385-397
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• 2020

This study investigated whether swimming exercises improves obesity through regulation of angiogenesis in white adipose tissue. Female mice with high-fat diets were divided into sham-operated group (Sham), ovariectomized group (OVX), and swim-trained ovariectomized group (OVX + Swim). Compared to the Sham, OVX increased body weight, adipose tissue mass and size of adipocyte. However, these factors (: such as body weight, adipose tissue mass and size of adipocyte) of OVX + Swim decreased compared with OVX. Compared with the Sham, OVX increased the mRNA expression of angiogenic activator and MMPs and decreased the mRNA expression of angiogenic inhibitors in white adipose tissue. But OVX + Swim decreased the mRNA expression of angiogenic activator and MMPs and increased the mRNA expression of angiogenic inhibitors in white adipose tissue, compared with the OVX. Theses results suggested that swimming exercises the angiogenesis in white adipose tissue, resulting to improve obesity in high-fat diet-fed female OVX mice.

• Journal of Animal Science and Technology
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• v.46 no.1
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• pp.7-14
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• 2004

The Stearoyl-CoA Desaturase(SCD) is a key enzyme, which converting palmitic acid(16:0) and stearic acid (18:0) to pahnitoleic acid(16:1) and oleic acid(l8:1), respectively. The concentration of oleic acid(18:1) in meat of beef cattle could influence both palatability and perception of meat. This experiment has conducted to determine relationship between the compositions of monounsaturated fatty acids and the SCD mRNA level in bovine liver and loin muscle tissue. The compositions of palmitoleic acid(16:1) and oleic acid(18:1) in loin muscle were 5% and 46% of total lipid and in liver were 2% and 20% of total lipid, respectively. On the other hand, the compositions of palmitic acid(16:0) and stearic acid(18:0) in loin muscle were 25% and 45% of total lipid and in liver were 14% and 43% of total lipid, respectively. The ratio of monounsaturated to saturated fatty acids(the desaturation index) was used as a measure of SCD activity in tissues. The average desaturation index in loin muscle was higher about 3.6-fold than that in liver. The desaturation index of oleate/stearate and palmitoleatelpalmitate in loin muscle were higher 8-fold and 1.8-fold than those in liver, respectively, showing that the substrate specificity of SCD enzyme was very different between liver and muscle tissues. To determine whether the composition of monounsaturated fatty acids in liver and muscle are dependent on SCD expression, SCD mRNA level was examined by RT-PCR analysis. The SCD mRNA level in loin muscle was higher about 3-fold than that in liver. Thus, the quantitative relationship between the desaturation index of fatty acid and SCD mRNA was observed in liver and muscle. The difference in the compositions of monounsaturated fatty acids between bovine liver and muscle tissues may be due to different level of Stearoyl-CoA Desaturase mRNA.

• Tuberculosis and Respiratory Diseases
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• v.54 no.5
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• pp.510-521
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• 2003

Background : The surfactant specific proteins, SP-B and SP-C are believed to be important regulators of the surfactant function and homeostasis. Since acute respiratory distress syndrome(ARDS) is usually viewed as the functional and morphological expression of a similar underlying lung injury caused by a variety of insults, and since abnormalities in the surfactant function have been described in ARDS, the authors investigated the different effects of endotoxin and thiourea on the accumulation of mRNA encoding SP-B and SP-C. Methods : Sprague-Dawley rats were given 5 mg/kg of an intraperitoneal endotoxin from Salmonella enteritidis and 3.5 mg/kg intraperitoneal thiourea and were sacrificed at different time periods. Results : 1. The SP-B mRNA levels 6 and 24 hours after the 5 mg/kg endotoxin treatment was significantly reduced by 26.1% and 50%, respectively(P<0.01, P<0.001). 2. The SP-B mRNA levels 24 hours after the 3.5 mg/kg thiourea treatment was reduced by 9.8% and 12.5%, respectively. 3. The SP-C mRNA levels 6 and 24 hours after the 5 mg/kg endotoxin treatment was significantly reduced by 38.7% and 53.6%, respectively(P<0.01, P<0.001). 4. The SP-C mRNA level 6 hours after the 3.5 mg/kg thiourea treatment was reduced by 22.8%(P<0.05). Conclusion : These results indicate that the differential regulation of the hydrophobic surfactant proteins in vivo is evident, and suggest that the hydrophobic surfactant proteins might be differentially regulated during lung injury at different time periods without altering the lung wet to dry ratios. The mechanism of these alternations at the different time periods and the different kinds of etiology remain to be determined.