• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.444-450
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• 2005

Epidermal growth factor (EGF) activates many intracellular effector molecules, which subsequently influence the expression levels of many genes involved in cell growth, apoptosis and signal transduction, etc. In this study, the early response of gene expressions due to EGF treatment was monitored using oligonucleotide DNA microarrays in rat schwannoma cell lines. An immunoblotting experiment showed the successful activation of EGF receptors and an effector protein, STAT5, due to EGF treatment. The microarray study showed that 35 genes were significantly induced and 2 were repressed within 60 min after the treatment. The list of induced genes included early growth response 1, suppressor of cytokine signaling 3, c-fos, interferon regulatory factor 1 and early growth response 2, etc. According to the microarray data, six of these were induced by more than 10-fold, and showed at least two different induction patterns, indicating complicated regulatory mechanisms in the EGF signal transduction.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.202-205
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• 2005

Cell phenotypes are determined by the concerted activity of thousands of genes and their products. This activity is coordinated by a complex network that regulates the expression of genes. Understanding this organization is crucial to elucidate cellular activities, and many researches have tried to construct gene regulatory networks from mRNA expression data which are nowadays the most available and have a lot of information for cellular processes. Several computational tools, such as Boolean network, Qualitative network, Bayesian network, and so on, have been applied to infer these networks. Among them, Bayesian networks that we chose as the inference tool have been often used in this field recently due to their well-established theoretical foundation and statistical robustness. However, the relative insufficiency of experiments with respect to the number of genes leads to many false positive inferences. To alleviate this problem, we had developed the algorithm of MONET(MOdularized NETwork learning), which is a new method for inferring modularized gene networks by utilizing two complementary sources of information: biological annotations and gene expression. Afterward, we have packaged and improved MONET by combining dispersed functional blocks, extending species which can be inputted in this system, reducing the time complexities by improving algorithms, and simplifying input/output formats and parameters so that it can be utilized in actual fields. In this paper, we present the architecture of MONET system that we have improved.

• Biomolecules & Therapeutics
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• 제23권2호
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• pp.110-118
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• 2015

According to the expansion of lifespan, neuronal disorder based on inflammation has been social problem. Therefore, we isolated shikonin from Lithospermum erythrorhizon and evaluated anti-inflammatory effects of shikonin in lipopolysaccharide (LSP)-stimulated BV2 microglial cells. Shikonin dose-dependently inhibits the expression of the proinflammatory mediators, nitric oxide (NO), prostaglandin $E_2$ ($PGE_2$), and tumor necrosis factor-${\kappa}B$ (TNF-${\alpha}$) as well as their main regulatory genes and products such as inducible NO synthase (iNOS), cyclooxygenase-2 (COX-2), and TNF-${\alpha}$ in LPS-stimulated BV2 microglial cells. Additionally, shikonin suppressed the LPS-induced DNA-binding activity of nuclear factor-${\kappa}B$ (NF-${\kappa}B$) to regulate the key regulatory genes of the proinflammatory mediators, such as iNOS, COX-2, and TNF-${\alpha}$, accompanied with downregulation of reactive oxygen species (ROS) generation. The results indicate that shikonin may downregulate the expression of proinflammatory genes involved in the synthesis of NO, $PGE_2$, and TNF-${\alpha}$ in LPS-treated BV2 microglial cells by suppressing ROS and NF-${\kappa}B$. Taken together, our results revealed that shikonin exerts downregulation of proinflammatory mediators by interference the ROS and NF-${\kappa}B$ signaling pathway.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.164-169
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• 2003

In this paper, we propose the integrated Bayesian network framework to reconstruct genetic regulatory networks from genome expression data. The proposed model overcomes the dimensionality problem of multivariate analysis by building coherent sub-networks from confined gene clusters and combining these networks via intermediary points. Gene Shaving algorithm is used to cluster genes that share a common function or co-regulation. Retrieved clusters incorporate prior biological knowledge such as Gene Ontology, pathway, and protein protein interaction information for extracting other related genes. With these extended gene list, system builds genetic sub-networks using Bayesian network with MDL score and Sparse Candidate algorithm. Identifying functional modules of genes is done by not only microarray data itself but also well-proved biological knowledge. This integrated approach can improve there liability of a network in that false relations due to the lack of data can be reduced. Another advantage is the decreased computational complexity by constrained gene sets. To evaluate the proposed system, S. Cerevisiae cell cycle data [1] is applied. The result analysis presents new hypotheses about novel genetic interactions as well as typical relationships known by previous researches [2].

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 추계학술대회
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• pp.33-33
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• 2018

This study was conducted to examine the role of the transcription factors (TFs) (RsMYB1 and mPAP1+B-Peru) in the regulation of anthocyanin biosynthesis in the ornamental torenia cv. Kauai rose. In this study, we could produce several putative transgenic lines overexpressing the TFs via Agrobacterium-mediated transformation, and presence of the TFs in the randomly selected five transgenic lines was confirmed using polymerase chain reaction (PCR). According to results of reverse transcription-PCR analysis (RT-PCR), the expression of the TFs in all transgenic lines and of the anthocyanin structural genes (CHS, F3H, DFR, and ANS) in all transgenic lines and WT plants were distinctly detectable. However, transcript levels of the structural genes expressed in the transgenic lines overexpressing TFs were significantly higher than those expressed in WT plants. Therefore, it is suggested that anthocyanin content in flowers of the transgenic torenia would be significantly higher than that in flowers of WT plants. Moreover, these results indicate that the TFs (RsMYB1 and mPAP1+B-Peru) could be exploited as potential anthocyanin regulatory TFs to enhance anthocyanin content in the other horticultural plants.

• 생명과학회지
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• 제21권1호
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• pp.159-164
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• 2011

미생물 세포 바이오센서는 환경오염물질의 모니터링을 위한 좋은 분석도구가 될 수 있다. 이는 리포터유전자들(예로, lux, gfp or lacZ)을 방향족 화합물이나 중금속과 같은 오염물질에 반응하는 유도 조절유전자와 결합하여 만든다. 이러한 유전자 재조합기술을 이용하여 많은 종류의 미생물 바이오센서가 개발되었으며 환경, 의학, 식품, 농업, 및 방위등 다양한 분야에서 활용되고 있다. 또한 바이오센서의 민감도와 검출범위는 조절유전자의 변형을 통해 증가시킬 수있다. 최근에는 미생물 바이오센서 세포를 고효율 검색용 세포 에레이의 칩, 광섬유 등에 고착하여 활용하고 있다. 본 논문은 특이 오염물질의 검출을 위한 유전자 재조합으로 만든 미생물 세포 바이오센서의 현황과 미래에 대해 고찰한다.

• Journal of Microbiology and Biotechnology
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• 제12권2호
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• pp.336-339
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• 2002

A total of 100 Corynebacterial clones exerting a regulatory effect on the aceB promoter of Corynebacterium glutamicum were isolated by utilizing a reporter carrying the enteric lacZ gene fused to the promoter. The isolated clones were classified into 3 groups of A, B, and C, according to their color of colonies. Escherichia coli cells carrying clones in groups A and B showed a $90\%\;and\;50\%$ reduction in ${\beta}$-galactosidase activity, respectively. The introduction of group A clones into C. glutamicum also resulted in an almost complete reduction in the expression of the aceA and aceB genes, suggesting that the clones express repressor-like proteins for the genes. Although white colonies were formed on plates containing X-gal, E. coli cells carrying one of the clones in group C exhibited intact ${\beta}$-galactosidase activity. The result suggests that the clone may encode proteins that prevent the cells from accumulating the chromogenic compound, X-gal.

• Molecules and Cells
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• 제42권2호
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• Genomics & Informatics
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• 제17권1호
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• pp.9.1-9.5
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• 2019

In previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. A basic hypothesis posited herein is that genomic regions carrying more functionally important sites will have a higher proportion of rare alleles. We estimated the proportions of rare single nucleotide polymorphisms with a minor allele frequency < 0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. As expected, rare alleles were found to be significantly enriched in most of the regulatory sites located in the first introns. Meanwhile, transcription factor binding sites were significantly more enriched in the 2-kb upstream regions (i.e., the regions of putative promoters of genes) than in the first introns. These results strongly support our proposal that the first intron sites of genes may have important regulatory functions in gene expression independent of promoters.

• Journal of Microbiology and Biotechnology
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• 제18권9호
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• pp.1485-1491
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• 2008

Tylosin biosynthesis is controlled in cascade fashion by multiple transcriptional regulators, acting positively or negatively, in conjunction with a signalling ligand that acts as a classical inducer. The roles of regulatory gene products have been characterized by a combination of gene expression analysis and fermentation studies, using engineered strains of S. fradiae in which specific genes were inactivated or overexpressed. Among various novel features of the regulatory model, involvement of the signalling ligand is not essential for tylosin biosynthesis.