• Biotechnology and Bioprocess Engineering:BBE
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• 제6권3호
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• pp.167-172
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• 2001

Staphylokinase (SAK) was produced in B. subtilis using two different promoter systems, i.e. the P43 and sacB promoters. To maximize SAK expression in B. subtilis, fermentation control strategies for each promoter were examined. SAK, under P43, a vegetative promoter transcribed mainly by $\sigma$(sup)B containing RNA polymerase, was overexpressed at low dissolved oxygen (D.O.) levels, suggesting that the sigB operon is somewhat affected by the energy charge of the cells. The expression of SAK at the 10% D.O. level was three times higher than that at the 50% D.O. level. In the case of sacB, a sucrose-inducible promoter, sucrose feeding was used to control the induction period and induction strength. Since sucrose is hydrolyzed by two sucrose hydrolyzing enzymes in the cell and culture broth, the control strategy was based on replenishing the loss of sucrose in the culture. With continuous feeding of sucrose, WB700 (pSAKBQ), which contains the SAK gene under sacB promoter, yielded ca. 35% more SAK than the batch culture. These results present efficient promoter-dependent control strategies in B. subtilis host system for foreign protein expression.

• Genomics & Informatics
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• 제14권2호
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• pp.46-52
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• 2016

Diverse somatic mutations have been reported to serve as cancer drivers. Recently, it has also been reported that epigenetic regulation is closely related to cancer development. However, the effect of epigenetic changes on cancer is still elusive. In this study, we analyzed DNA methylation data on colon cancer taken from The Caner Genome Atlas. We found that several promoters were significantly hypermethylated in colon cancer patients. Through clustering analysis of differentially methylated DNA regions, we were able to define subgroups of patients and observed clinical features associated with each subgroup. In addition, we analyzed the functional ontology of aberrantly methylated genes and identified the G-protein-coupled receptor signaling pathway as one of the major pathways affected epigenetically. In conclusion, our analysis shows the possibility of characterizing the clinical features of colon cancer subgroups based on DNA methylation patterns and provides lists of important genes and pathways possibly involved in colon cancer development.

• 환경영향평가
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• 제19권2호
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• pp.141-151
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• 2010

It has been pointed out that the process of environmental impact assessment in Korea has been less of equity and balance between stakeholders, and less of objective validity in writing impact statement and in holding consultations. Thus this study has intended to find improvement measures regarding the processes of EIS documentation and holding consultations between stakeholders during environmental impact assessment process. To achieve this goal this study carried out expert survey method to analyze validity and suitability of suggested measures in accordance with the problems found through reviewing related literatures. This study has found major improvement measures including transferring the responsibility to write impact statement and to hold consultations from project promoters to the third party (impact assessment committee) composed of related stakeholders without project promoters. The developers need to pay for all expenses to proceed impact assessment.

• Journal of Microbiology and Biotechnology
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• 제8권3호
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• pp.280-283
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• 1998

We have cloned the RNA polymerase sigma-like factors from a wide range of actinomycetes by using specific primers with the polymerase chain reaction (PCR). The specific oligonucleotide primers were designed on the basis of amino acid sequences of conserved regions from HrdA, B, D of Streptomyces griseus as well as from the rpoD box of many eubacteria. The consensus sequences were from the rpoD box and helix-turn-helix motif involved in -35 recognition. The designed primers were successfully applied to amplify the DNA fragments of the hrd homolog genes from 8 different strains of actinomycetes which produce a wide variety of important antibiotics. The 480 bp of the DNA fragment was amplified from all 8 strains, and it was identified as a part of hrdA and hrdB as we designed. The deduced amino acid sequence of PCR-amplified DNA fragments were highly homologous to those of other known RNA polymerase sigma factors of S. griseus and Streptomyces aureofaciens. Therefore, this study with specifically designed primers will support rapid cloning of the RNA polymerase sigma factors which recognize different classes of promoters from actinomycetes, and it will also be helpful in understanding the relationship of promoters and sigma factors leading to heterogeneity of RNA polymerases in actinomycetes.

• 한국표면공학회지
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• 제23권2호
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• pp.30-38
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• 1990

For the purpose of suggesting the thermal resistant catalyst for automobile emission control, various catalysts, Pd-WO3 and PD-La2O3 systems, were charactrized before and after thermal aging. It was found that La2O3 formed amorphous surface compound on the support by strong metal-support interaction(SMSI). And by Temperature Programmed Desorption (TPD) expeiment, it was found that the distribution of acid site which is strong acid sites by adding the promoters. After thermal aging, it was observed that the acidity of Pd-WO3 system was decreased largely because of losing acid site by metal vaporization. On the other hand, there was pretty small change in the properties of matter of Pd-La2O3 system. Therefore, it could be considered that La2O3 formed heat resisting amorphous surface compound on the support by SMSI.

• Journal of Microbiology
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• 제43권5호
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• pp.411-416
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• 2005

The high-throughput sequencing of microbial genomes has resulted in the relatively rapid accumulation of an enormous amount of genomic sequence data. In this context, the problem posed by the detection of promoters in genomic DNA sequences via computational methods has attracted considerable research attention in recent years. This paper addresses the development of a predictive model, known as the dependence decomposition weight matrix model (DDWMM), which was designed to detect the core promoter region, including the -10 region and the transcription start sites (TSSs), in prokaryotic genomic DNA sequences. This is an issue of some importance with regard to genome annotation efforts. Our predictive model captures the most significant dependencies between positions (allowing for non­adjacent as well as adjacent dependencies) via the maximal dependence decomposition (MDD) procedure, which iteratively decomposes data sets into subsets, based on the significant dependence between positions in the promoter region to be modeled. Such dependencies may be intimately related to biological and structural concerns, since promoter elements are present in a variety of combinations, which are separated by various distances. In this respect, the DDWMM may prove to be appropriate with regard to the detection of core promoter regions and TSSs in long microbial genomic contigs. In order to demonstrate the effectiveness of our predictive model, we applied 10-fold cross-validation experiments on the 607 experimentally-verified promoter sequences, which evidenced good performance in terms of sensitivity.

• 대한기계학회논문집B
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• 제30권5호
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• pp.389-396
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• 2006

For the successful design of heat exchangers, it is very important to understand local heat transfer phenomena on the circular tube of heat exchangers. In the present study, experiments are performed for single circular tube and tube banks with and without heat transfer promoters. The naphthalene sublimation technique is employed to measure the local mass transfer coefficients, and the measured local mass transfer data are converted to the local heat transfer data using heat and mass transfer analogy. The distribution pattern of local Nusselt numbers on single circular tube with heat transfer promoters is similar to that without the heat transfer promoter, but average Nusselt numbers are greatly increased. In case of tube banks without the heat transfer promoter, the Nusselt numbers are much lower in the first row than those of other rows, but the local heat transfer coefficients on all rows are equalized when the heat transfer promoter is installed.

• Nuclear Engineering and Technology
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• 제51권5호
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• pp.1251-1260
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• 2019

The water-cooled WCLL blanket is one of the possible candidates for the blanket of the fusion power reactors. The plasma-facing first wall manufactured from the reduced-activation ferritic-martensitic steel Eurofer97 will be cooled with water at a typical pressurized water reactor (PWR) conditions. According to new estimates, the first wall will be exposed to peak heat fluxes up to $7MW/m^2$ while the maximum operated temperature of Eurofer97 is set to $550^{\circ}C$. The performed analysis shows the capability of the designed flat first wall concept to remove heat flux without exceeding the maximum Eurofer97 operating temperature only up to $0.75MW/m^2$. Several heat transfer enhancement methods (turbulator promoters), structural modifications, and variations of parameters were analysed. The effects of particular modifications on the wall temperature were evaluated using thermo-hydraulic three-dimensional numerical simulation. The analysis shows the negligible effect of the turbulators. By the combination of the proposed modifications, the permitted heat flux was increased up to $1.69MW/m^2$ only. The results indicate the necessity of the re-evaluation of the existing first wall concepts.

• 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.

• Molecules and Cells
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• 제45권8호
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• pp.522-530
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• 2022

Transposable elements (TEs) account for approximately 45% of the human genome. TEs have proliferated randomly and integrated into functional genes during hominoid radiation. They appear as right-handed B-DNA double helices and slightly elongated left-handed Z-DNAs. Human endogenous retrovirus (HERV) families are widely distributed in human chromosomes at a ratio of 8%. They contain a 5'-long terminal repeat (LTR)-gag-pol-env-3'-LTR structure. LTRs contain the U3 enhancer and promoter region, transcribed R region, and U5 region. LTRs can influence host gene expression by acting as regulatory elements. In this review, we describe the alternative promoters derived from LTR elements that overlap Z-DNA by comparing Z-hunt and DeepZ data for human functional genes. We also present evidence showing the regulatory activity of LTR elements containing Z-DNA in GSDML. Taken together, the regulatory activity of LTR elements with Z-DNA allows us to understand gene function in relation to various human diseases.