• 한국정보과학회논문지:소프트웨어및응용
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• 제31권4호
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• pp.525-536
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• 2004

유전발현 데이타는 생명체의 특정 조직에서 채취한 샘플을 microarray상에서 측정한 것으로, 유전자들의 발현 정도가 수치로 나타난 데이타이다. 일반적으로 정상조직과 이상조직에서 관련 유전자들의 발현정도는 차이를 보이기 때문에, 유전발현 데이타를 통하여 질병을 분류할 수 있다. 이러한 분류에 모든 유전자들이 관여하지는 않으므로 관련 유전자를 선별하는 작업인 특징선택이 필요하며, 선택된 유전자들을 적절히 분류하는 방법이 필요하다. 본 논문에서는 상관계수, 유사도, 정보이론 등에 기반을 둔 7가지 특징선택 방법과 대표적인 6가지 분류기에 대하여 특징-분류기 쌍의 최적 앙상블을 탐색하기 위한 유전자 알고리즘 기반 방법을 제안한다. 두 가지 암 관련 유전자 발현 데이타에 대하여 leave-one-out cross validation을 포함한 실험을 해본 결과, 림프종 데이타와 대장암 데이타 모두 단일 특징-분류기 쌍보다 훨씬 우수한 성능을 보이는 앙상블들을 발견할 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제19권3호
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• pp.329-334
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• 2006

Adipocyte-specific secretory factor (ADSF)/resistin, a hormone, is a small cysteine-rich protein secreted from adipose tissue and has been implicated in modulating adipogenesis in humans and rodents. The objective of this study was to clone a gene encoding ADSF/resistin and to characterize its function in Korean Native Cattle (Hanwoo). The coding sequence was 330 base pairs and it encoded a protein of 109 amino acids. An NCBI BLAST-search revealed the cloned cDNA fragment shared significant homology (82%) with the cDNA encoding the human ADSF/resistin. The nucleotide sequence homology of the Hanwoo sequence was 73% and 64% for the rat and mouse, respectively. A 654 bp ADSF/resistin gene promoter was cloned and putative binding sites of transcription factors were identified. Tissue distribution of ADSF mRNA was examined in liver, skeletal muscles (tenderloin, biceps femoris), subcutaneous fat, and perirenal fat by RT-PCR. ADSF mRNAs were detected in fat tissues but not in liver and muscles, suggesting that ADSF/resistin expression may be induced during adipogenesis. Although, the physiological function of ADSF/resistin in the cow remains to be determined, these data indicate ADSF is related to the adipocyte phenotype and may have a possibly regulatory role in adipocyte function.

• Biomolecules & Therapeutics
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• 제22권6호
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• pp.497-502
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• 2014

In the present study, we found that the natural compound arctigenin inhibited hydrogen peroxide-induced reactive oxygen species (ROS) production in rat primary astrocytes. Since hemeoxygenase-1 (HO-1) plays a critical role as an antioxidant defense factor in the brain, we examined the effect of arctigenin on HO-1 expression in rat primary astrocytes. We found that arctigenin increased HO-1 mRNA and protein levels. Arctigenin also increases the nuclear translocation and DNA binding of Nrf2/c-Jun to the antioxidant response element (ARE) on HO-1 promoter. In addition, arctigenin increased ARE-mediated transcriptional activities in rat primary astrocytes. Further mechanistic studies revealed that arctigenin increased the phosphorylation of AKT, a downstream substrate of phosphatidylinositol 3-kinase (PI3K). Treatment of cells with a PI3K-specific inhibitor, LY294002, suppressed the HO-1 expression, Nrf2 DNA binding and ARE-mediated transcriptional activities in arctigenin-treated astrocyte cells. The results collectively suggest that PI3K/AKT signaling pathway is at least partly involved in HO-1 expression by arctigenin via modulation of Nrf2/ARE axis in rat primary astrocytes.

• Asian Pacific Journal of Cancer Prevention
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• 제13권11호
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• pp.5563-5568
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• 2012

Based on our previous report on gastric cancer which documented ATP4A and ATP4B mRNA down-regulation in gastric tumors relative to normal gastric tissues, we hypothesized that epigenetic mechanisms could be responsible. ATP4A and ATP4B mRNA expression in gastric cancer cell lines AGS, SNU638 and NUGC-3 was examined using reverse transcriptase PCR (RT-PCR). AGS cells were treated with TSA or 5'-AzaDC and methylation specific PCR (MSP) and bisulfite sequencing PCR (BSP) analysis were performed. MSP analysis was on DNA from paraffin embedded tissues sections and plasma. Expression analysis revealed downregulation of ATP4A and ATP4B genes in gastric cancer cell lines relative to normal gastric tissue, while treatment with 5'-AzaDC re-activated expression of both. Search for CpG islands in their putative promoter regions did not indicate CpG islands (CGI) but only further downstream in the bodies of the genes. Methylation specific PCR (MSP) in the exon1 of the ATP4B gene and exon7 in ATP4A indicated methylation in all the gastric cancer cell lines tested. MSP analysis in tumor tissue samples revealed methylation in the majority of tumor samples, 15/19, for ATP4B and 8/8 for ATP4A. There was concordance between ATP4B and ATP4A down-regulation and methylation status in the tumour samples tested. ATP4B methylation was detectable in cell free DNA from gastric cancer patient's plasma samples. Thus ATP4A and ATP4B down-regulation involves DNA methylation and methylated ATP4B DNA in plasma is a potential biomarker for gastric cancer.

• BMB Reports
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• 제29권2호
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• pp.146-150
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• 1996

A 2.1 kb cDNA clone for rat transketolase was isolated from rat liver ${\lambda}gt11$ cDNA library and its sequence was determined. The predicted rat transketolase (655 amino acids with $M_r$ 71,186) is highly similar (92%) to that of the human enzyme except that it contains an extra 32 amino acids at its N-terminus. Although it is less similar (<27%) to transketolases from non-mammalian species, the functional motifs such as the catalytic sites and thiamine binding domain are well conserved in the rat enzyme. Southern blot analysis of genomic DNA verified that transketolase appears to be derived from a single gene. Immunoblot and Northern blot analyses suggested that hepatic transketolase was activated pretranslationally by a 2.1-fold while little change was observed in brain enzyme, indicating a tissue-specific pretranslational activation during postnatal development.

• Fisheries and Aquatic Sciences
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• 제22권12호
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• pp.28.1-28.8
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• 2019

Background: In the present study, we evaluated four commonly used housekeeping genes, viz., actin-β, elongation factor-1α (EF1α), acidic ribosomal protein (ARP), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as internal references for quantitative analysis of immune genes in nervous necrosis virus (NNV)-infected seven-band grouper, Hyporthodus septemfasciatus. Methods: Expression profiles of the four genes were estimated in 12 tissues of healthy and infected seven-band grouper. Expression stability of the genes was calculated using the delta Ct method, BestKeeper, NormFinder, and geNorm algorithms. Consensus ranking was performed using RefFinder, and statistical analysis was done using GraphpadPrism 5.0. Results: Tissue-specific variations were observed in the four tested housekeeping genes of healthy and NNV-infected seven-band grouper. Fold change calculation for interferon-1 and Mx expression using the four housekeeping genes as internal references presented varied profiles for each tissue. EF1α and actin-β was the most stable expressed gene in tissues of healthy and NNV-infected seven-band grouper, respectively. Consensus ranking using RefFinder suggested EF1α as the least variable and highly stable gene in the healthy and infected animals. Conclusions: These results suggest that EF1α can be a fairly better internal reference in comparison to other tested genes in this study during the NNV infection process. This forms the pilot study on the validation of reference genes in Hyporthodus septemfasciatus, in the context of NNV infection.

• Fisheries and Aquatic Sciences
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• 제15권3호
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• pp.221-231
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• 2012

The marine medaka Oryzias dancena choriogenin H gene (odChgH) and its mRNA expression during estradiol-$17{\beta}$ (E2) exposure were characterized. At the amino acid level, the choriogenin H protein is predicted to possess the conserved repetitive N-terminal region, as well as zona pellucida (ZP) and Trefoil factor family (TFF) domains. At the genomic level, odChgH has an eight-exon organization with a distribution pattern of transcription factor binding sites in the 5'-upstream region, which is commonly found in other estrogen-responsive genes. The tissue distribution pattern of odChgH mRNA was found to be gender-specific, whereby females showed a higher expression level and wider tissue distribution than did males. During embryonic development, odChgH mRNA was robustly detected from the stage of visceral blood vessel formation. Experimental E2 exposure of males resulted in odChgH mRNA being induced not only in the liver, but also in other several tissues. The E2-mediated induction was fairly dose-dependent. The basal expression levels of hepatic odChgH mRNA were lower in males that were acclimated to 30 ppt salinity than in those acclimated to 0 or 15 ppt salinity. In contrast, the inducibility of odChgH mRNA during E2 exposure was greater in seawater-acclimated fish than in brackish water- or freshwater-acclimated fish.

• Asian-Australasian Journal of Animal Sciences
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• 제30권3호
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• pp.328-337
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• 2017

Objective: An experiment was conducted to determine the relationship between the KAP11.1 and the regulation wool fineness. Methods: In previous work, we constructed a skin cDNA library and isolated a full-length cDNA clone termed KAP11.1. On this basis, we conducted a series of bioinformatics analysis. Tissue distribution of KAP11.1 mRNA was performed using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis. The expression of KAP11.1 mRNA in primary and secondary hair follicles was performed using real-time PCR (real-time polymerase chain reaction) analysis. The expression location of KAP11.1 mRNA in primary and secondary hair follicles was performed using in situ hybridization. Results: Bioinformatics analysis showed that KAP11.1 gene encodes a putative 158 amino acid protein that exhibited a high content of cysteine, serine, threonine, and valine and has a pubertal mammary gland) structural domain. Secondary structure prediction revealed a high proportion of random coils (76.73%). Semi-quantitative RT-PCR showed that KAP11.1 gene was expressed in heart, skin, and liver, but not expressed in spleen, lung and kidney. Real time PCR results showed that the expression of KAP11.1 has a higher expression in catagen than in anagen in the primary hair follicles. However, in the secondary hair follicles, KAP11.1 has a significantly higher expression in anagen than in catagen. Moreover, KAP11.1 gene has a strong expression in inner root sheath, hair matrix, and a lower expression in hair bulb. Conclusion: We conclude that KAP11.1 gene may play an important role in regulating the fiber diameter.

• BMB Reports
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• 제47권2호
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• pp.86-91
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• 2014

Tissue-specific gene expression is regulated by epigenetic modification involving trans-acting factors. Here, we identified that the human MAGEB16 gene and its mouse homolog, Mageb16, are only expressed in the testis. To investigate the mechanism governing their expression, the promoter methylation status of these genes was examined in different samples. Two CpG islands (CGIs) in the 5' upstream region of MAGEB16 were highly demethylated in human testes, whereas they were methylated in cells without MAGEB16 expression. Similarly, the CGI in Mageb16 was hypomethylated in mouse testes but hypermethylated in other tissues and cells without Mageb16 expression. Additionally, the expression of these genes could be activated by treatment with the demethylation agent 5'-aza-2'-deoxycytidine (5'-aza-CdR). Luciferase assays revealed that both gene promoter activities were inhibited by methylation of the CGI regions. Therefore, we propose that the testis-specific expression of MAGEB16 and Mageb16 is regulated by the methylation status of their promoter regions.

• 생명과학회지
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• 제34권3호
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• pp.199-207
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• 2024

CYP 효소는 내인성 및 외인성 화학물질의 대사에 핵심적인 역할을 담당한다. 특히, 약물, 자연생성물 및 환경 독성 화학물질 등은 조직에 따라 특이적 CYP 효소 유전자의 발현을 조절하며, 이는 체내 유입된 약물과 독성물질 등과 같은 화학물질들 사이의 상호작용을 유발하여 이들의 대사에 영향을 줌으로써, 결국 치료 효과와 독성 효과에 변화를 초래한다. 이 분야에 대한 지난 수십 년 동안의 집중적인 연구는, 이러한 CYP 효소 유전자의 발현조절을 매개하는 분자적 기전을 이해하는 데 상당한 진전을 가져왔다. 이제는 구체적인 CYP 효소 유전자의 발현 유도를 조절하는 화합물들뿐만 아니라, 이를 감지하여 특정 CYP 유전자의 발현 조절을 매개하는 데 관여하는 수용체들과 이들의 신호전달 경로들이 비교적 상세히 밝혀졌다. 본 총설에서는, 다양한 화학물질의 노출에 반응하여 CYP 효소 유전자들의 발현 유도를 매개하는 것으로 알려진 주요 외인성 물질-감지 수용체들과 기타 조절인자들의 분자적 작용기전을 요약한다.