• 한국응용약물학회:학술대회논문집
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• 한국응용약물학회 1995년도 제3회 추계심포지움
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• pp.9-15
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• 1995

When quiescent cells ate stimulated to enter the cell cycle, the thymidine kinase(TK) gene is transcriptionally activated at the border of Gl and 5. In this report we show that the human TK promoter contains multiple protein-binding sites. By site-directed mutagenesis, we identified a protein-binding site on the human TK promoter requited for conferring Gl-S-regulated transcription to a heterologous promoter and dissociated it functionally from an adjacent protein-binding domain containing an inverted CCAAT motif requited for high basal level expression. Substitution-mutation of this site results in constitutive expression of the neo reporter gene in serum-stimulated fibroblasts, as well as in cells arrested in mid-Gl by a temperature-sensitive mutation. The regulatory domains for the human TK promoter exhibit interesting symmetrical features, including a set of CCAAT motifs and sites similar to the novel Yi protein-binding site recently discovered in the mouse TK promoter. Thus, components of the hTK complex is important for hTK gene regulation.

• Asian Pacific Journal of Cancer Prevention
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• 제15권7호
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• pp.3145-3149
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• 2014

Gene expression profiling facilitates the understanding of biological characteristics of gliomas. Previous studies mainly used regression/variance analysis without considering various background biological and environmental factors. The aim of this study was to investigate gene expression differences between grade III and IV gliomas through partial least squares (PLS) based analysis. The expression data set was from the Gene Expression Omnibus database. PLS based analysis was performed with the R statistical software. A total of 1,378 differentially expressed genes were identified. Survival analysis identified four pathways, including Prion diseases, colorectal cancer, CAMs, and PI3K-Akt signaling, which may be related with the prognosis of the patients. Network analysis identified two hub genes, ELAVL1 and FN1, which have been reported to be related with glioma previously. Our results provide new understanding of glioma pathogenesis and prognosis with the hope to offer theoretical support for future therapeutic studies.

• Journal of Microbiology
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• 제44권2호
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• pp.248-253
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• 2006

Lymphocystis disease virus (LCDV) is the causative agent of lymphocystis disease. The viruses have been divided into three genotypes (genotype I for LCDV-1, II for Japanese flounder isolates, and III for rockfish isolates) on the basis of major capsid protein (MCP) gene sequences. In this study, we developed a multiplex PCR primer set in order to distinguish these genotypes. We also analyzed the MCP gene of a new LCDV isolate from the sea bass (SB98Yosu). Comparison of sequence identities between SB98Yosu and eight Japanese flounder isolates, revealed identity of more than 90.1 % at nucleotide level and 96.5% at deduced amino acid level, respectively. Phylogenetic analyses based on the MCP gene showed that SB98Yosu belongs to genotype II, along with Japanese flounder isolates. Multiplex PCR based on the MCP gene allowed us to identify these genotypes in a simple and rapid manner, even in a sample that contained two genotypes, in this case genotypes II and III.

• 한국식품과학회지
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• 제32권6호
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• pp.1331-1335
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• 2000

김치 젖산균인 WL6는 API kit 또는 Biolog system방법에 의하여 동정한 결과, Leuconostoc mesenteroides ssp. cremoris, Leu. mesenteroides ssp. dextranicum 또는 Lactobacillus bifermentans로 나타나 동정되지 않았다. 그러나, pepN gene과 16S rRNA gene으로부터 2개의 specific-sequence primer set을 제조하여 PCR 방법으로 증폭한 후에 표준균주들과 비교한 결과, WL6는 Lactobacillus bifermentans로 추정되었다.

• Animal cells and systems
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• 제5권2호
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• pp.101-106
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• 2001

AFLPS (amplified fragment length polymorphisms) were used to estimate the genetic diversity of seven populations of Brassica campestis L. ssp. napus var. nippo-oleifera Makino between naturalized and cultivated populations. The seven Korean populations maintained a high level of genetic diversity. For example, all eight primers were high polymorphic, with an average of 3.2 effective alleles per primer set, and the expected heterozygosity was also high. The majority of genetic variance resided within populations The combinations of an insect-pollinated, outcrossing breeding system, large populations sizes, a high degree of gene flow and a propensity for high fecundity may explain the high level of genetic diversity within cultivated populations. Estimates of genetic similarity on the proportion of shared fragments ranged from 0.952 to 0.999. The high level of gene flow In Korean naturalized populations is mainly caused by seed dispersal via sea tide and the gene flow of cultivated populations may be enhanced in part by artificial pollen dispersal.

• 생명과학회지
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• 제19권8호
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• pp.1159-1163
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• 2009

ER stress에 관련된 유전자의 기능변화와 전사조절인자 분석하기 위해 ER stress를 유도한 간세포에서 expression microarray로 유전자 발현을 확보한 후 GSECA로 분석하였다. ER stress가 유도되면, ER에 주어지는 과도한 부하를 감소시키는 기능들이 증가하는 반면, ER stress가 더 증가함에 따라 ATP 생성이나 DNA repair, 더 나아가 세포분열의 기능이 감소하는 등 세포가 damage을 받음을 알 수 있었다. ER stress에 관련된 전사조절인자로는 FOX04, AP-1, FOX03, HNF4, IRF-1, GATA 등의 전사조절인자들이 ER stress에 의해 발현이 증가하는 유전자들의 promoter에 공통적으로 존재하였으며, E2F, Nrf-1, Elk-1, YY1, CREB, MTF-1, STAT-1, ATF 등의 전사인자들이 발현이 감소하는 유전자들의 promoter에서 공통적으로 존재하여, 이들의 전사인자들이 ER stress에 의한 유전자의 발현조절에 중요한 역할을 하는 전사조절인자임을 알 수 있었다.

• 정보처리학회논문지D
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• 제12D권5호
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• pp.755-764
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• 2005

생명체의 주된 기능 요소인 유전자를 모두 식별하는 작업의 중요성이 증가함에 따라, 최근에 유전자 예측도구들이 활발히 개발되고 있다. 그러나 유전자 예측 프로그램들은 예측 결과를 그들 고유의 형식으로 제공하여 사용자가 그 결과를 이해하기 위해서는 상당히 많은 추가적인 노력이 필요하다. 따라서 유전자 예측결과에 대한 표준화된 표현과 유전자 데이터 집합에 대한 예측결과를 자동으로 계산하는 방법을 지원하는 것이 바람직하다. 본 논문에서는 다양한 유전자 예측 정보에 대한 효과적인 XML 표현과 이를 바탕으로 예측된 유전자 결과를 자동으로 분석하는 in 기반 분석 도구에 대하여 기술한다. 개발된 도구는 유전자 예측도구를 사용하는 사용자들이 편리하게 예측결과를 분석하고 예측결과에 대한 통계결과를 자동으로 산출할 수 있도록 지원한다. 도구의 유용성을 보여주기 위하여 널리 사용되는 유전자 예측 도구인 GenScan과 GeneID의 처리결과를 개발된 도구에 적용시켜 보았다.

• Molecules and Cells
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• 제46권1호
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• pp.65-67
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• 2023

SMILES (simplified molecular-input line-entry system) information of small molecules parsed by one-hot array is passed to a convolutional neural network called black box. Outputs data representing a gene signature is then matched to the genetic signature of a disease to predict the appropriate small molecule. Efficacy of the predicted small molecules is examined by in vivo animal models. GSEA, gene set enrichment analysis.

• Journal of Microbiology and Biotechnology
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• 제20권2호
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• pp.245-253
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• 2010

The base sequences representing human- and cow-specific 168 rRNA gene markers identified in a T-RFLP analysis were recovered from clone libraries. The human- and cow-specific primers were designed from these sequences and their specificities were analyzed with fecal DNAs from human, cow, and pig. The AllBac primer set showed positive results for all human, cow, and pig samples, whereas the human-specific primer set showed positive result only for the human sample but not for the cow or pig samples. Likewise, the cow-specific primer set showed positive results only for the cow sample but not for the human or pig samples. Real-time PCR assay with these primers was developed for the identification and quantification of fecal pollution in the river water. The human- and cow-specific markers were detected in the order of 9 $\log_{10}$ copies per gram wet feces, which were two orders of magnitude lower than those of total Bacteroidales. For the river water samples, the human-specific marker was detected in $1.7-6.2\;\log_{10}$ copies/100 ml water, which was 2.4-4.9 orders of magnitude lower than those of total Bacteroidales. There was no significant correlation between total Bacteroidales and conventional fecal indicators, but there was a high correlation between Bacteroidales and the human-specific marker. This assay could reliably identify and quantify the fecal pollution sources, enabling effective measures in the watersheds and facilitating water quality management.

• Asian Pacific Journal of Cancer Prevention
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• 제15권21호
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• pp.9367-9373
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• 2014

In diagnosis of lung cancer, rapid distinction between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) tumors is very important. Serum markers, including lactate dehydrogenase (LDH), C-reactive protein (CRP), carcino-embryonic antigen (CEA), neurone specific enolase (NSE) and Cyfra21-1, are reported to reflect lung cancer characteristics. In this study classification of lung tumors was made based on biomarkers (measured in 120 NSCLC and 60 SCLC patients) by setting up optimal biomarker joint models with a powerful computerized tool - gene expression programming (GEP). GEP is a learning algorithm that combines the advantages of genetic programming (GP) and genetic algorithms (GA). It specifically focuses on relationships between variables in sets of data and then builds models to explain these relationships, and has been successfully used in formula finding and function mining. As a basis for defining a GEP environment for SCLC and NSCLC prediction, three explicit predictive models were constructed. CEA and NSE are requentlyused lung cancer markers in clinical trials, CRP, LDH and Cyfra21-1 have significant meaning in lung cancer, basis on CEA and NSE we set up three GEP models-GEP 1(CEA, NSE, Cyfra21-1), GEP2 (CEA, NSE, LDH), GEP3 (CEA, NSE, CRP). The best classification result of GEP gained when CEA, NSE and Cyfra21-1 were combined: 128 of 135 subjects in the training set and 40 of 45 subjects in the test set were classified correctly, the accuracy rate is 94.8% in training set; on collection of samples for testing, the accuracy rate is 88.9%. With GEP2, the accuracy was significantly decreased by 1.5% and 6.6% in training set and test set, in GEP3 was 0.82% and 4.45% respectively. Serum Cyfra21-1 is a useful and sensitive serum biomarker in discriminating between NSCLC and SCLC. GEP modeling is a promising and excellent tool in diagnosis of lung cancer.