• Interdisciplinary Bio Central
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• v.4 no.3
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• pp.10.1-10.12
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• 2012

Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.

• Biomedical Science Letters
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• v.7 no.3
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• pp.103-110
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• 2001

$\alpha$-Fetoprotein(AFP) is a good marker for the detection of several diseases such as hepatocellular carcinoma, gonadal germ cell tumor, gastric tumor, and Down's syndrome. In this study, we developed ELISA, using synthetic peptides corresponding to the epitopes of AFP. Five kinds of peptides were synthesized from AFP to produce antibodies in rats that recognize AFP in human plasma as well as amniotic fluid and do not cross-react with serum albumin. All five kinds of antibodies showed good reactivities with their peptide-keyhole limpet hemocyanin conjugates. Anti-synthetic peptide 1 (R-N-E-Y-G-I-A-S-I-L, 4-13) antibody, in particular, reacted well with AEP as well as synthetic peptide 1-KLH but not with human serum albumin. The binding affinity(Kd) was 2.7$\times$10$^{-9}$M for peptide 1 and 6.8$\times$10$^{-8}$M for AEP. The range for measurement of AFP was 10~1,000 ng/ml. The within-assay and between-assay coefficients of variance(CV) were 4.83% and 10.97%, respectively. In a sample of 31 sera and 33 amniotic fluids, there was a good correlation between AFP values determined in this assay and those in a commercial kit. These results indicate that the antibodies against synthetic peptides corresponding to the epitopes of AFP are highly specific to APP and synthetic peptide-based ELISA would be useful for the measurement of human AFP.

• Journal of the Korean Chemical Society
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• v.59 no.2
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• pp.188-193
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• 2015

• Journal of Microbiology
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• v.45 no.4
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• pp.344-349
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• 2007

We have isolated previously three synthetic lethal mutants in Schizosaccharomyces pombe, which genetically interact with mex67, in order to identify the genes involved in mRNA export. A novel nup97 gene was isolated by complementation of the growth defect in one of the synthetic lethal mutants, SLMex3. The nup97 gene contains one intron and encodes an 851 amino-acid protein that is similar to nucleoporins, Nppl06p in S. pombe and Nic96p in Saccharomyces cerevisiae. The nup97 gene is essential for vegetative growth, and nup97 null mutant harboring pREP41X-Nup97 showed $poly(A)^+$ RNA export defect when expression of nup97 is repressed in the presence of thiamine. These results suggest that nup97 is involved in mRNA export from the nucleus to cytoplasm.

• Proceedings of the Zoological Society Korea Conference
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• 1998.10b
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• pp.361.1-361
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• 1998

No Abstract, See Full Text

• Bulletin of the Korean Chemical Society
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• v.27 no.10
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• pp.1567-1571
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• 2006

Synthetic color additives approved for general food use are sixteen in European Union, seven in U. S. A. and twelve in Japan. Twelve food dyes were examined for their inhibitory potency against human protein tyrosine phosphatases (PTPases). Half of the food colorants inhibited PTPases significantly and three of them were potent inhibitors with low micromolar IC50 values. Also examined were the synthetic dyes structurally similar but not allowed in food. Some of them were potent inhibitors of PTPases. Considering the importance of PTPases in cellular signal transduction, inhibition of PTPases by food colorants might cause harmful effects in human health.

• Journal of Science and Technology Studies
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• v.14 no.2
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• pp.85-125
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• 2014

This paper explores what we call 'the problem of undone social science' by examining the lack of interests in the social, ethical, and legal issues of synthetic biology among social scientists in Korea. This new field of science, which has emerged in the twenty-first century with the promise of solving future problems of energy, food, and disease in the world, has also created a considerable degree of anxiety over the issues of bioethics, biosafety, and biosecurity. From its beginning, therefore, researchers of synthetic biology in Europe and the U.S. have sought to engage social scientists in their projects. Yet scientists and social scientists in Korea have shown no sign of working together to deal with both potential benefits and risks of synthetic biology. Why this silence? What strategic moves would be needed to overcome the structural barrier for their collaboration? Surveying the diverse methodologies developed during and after ELSI (ethical, legal, social implications) experiments, this paper aims to provide three suggestions that might make possible mutually profitable and continuously stimulating dialogues between the two worlds of science and social science: first, institutionalize the ELSI studies on any newly emerging science and technology of concern; second, explore diverse post-ELSI methodologies experimented elsewhere and develop ones that might be applicable best to the Korean situation; and third and perhaps most important, create an intellectual space and a lawful protection for social scientists to exercise their research freedom at the reasonable level and receive a fair review by their peers, not solely by funding agencies and scientific organizations.

• BMB Reports
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• v.48 no.9
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• pp.489-494
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• 2015

The in vitro antibody discovery technologies revolutionized the generation of target-specific antibodies that traditionally relied on the humoral response of immunized animals. An antibody library, a large collection of diverse, pre-constructed antibodies, can be rapidly screened using in vitro display technologies such as phage display. One of the keys to successful in vitro antibody discovery is the quality of the library diversity. Antibody diversity can be obtained either from natural B-cell sources or by the synthetic methods that combinatorially generate random nucleotide sequences. While the functionality of a natural antibody library depends largely upon the library size, various other factors can affect the quality of a synthetic antibody library, making the design and construction of synthetic antibody libraries complicated and challenging. In this review, we present various library designs and diversification methods for synthetic antibody library. From simple degenerate oligonucleotide synthesis to trinucleotide synthesis to physicochemically optimized library design, the synthetic approach is evolving beyond the simple emulation of natural antibodies, into a highly sophisticated method that is capable of producing high quality antibodies suitable for therapeutic, diagnostic, and other demanding applications. [BMB Reports 2015; 48(9): 489-494]

• Interdisciplinary Bio Central
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• v.4 no.1
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• pp.2.1-2.7
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• 2012

Introduction: Histone deacetylases (HDAC) are a class of enzymes that remove acetyl groups from ${\varepsilon}$-N-acetyl lysine amino acids of histone proteins. Their action is opposite to that of histone acetyltransferase that adds acetyl groups to these lysines. Only few HDAC inhibitors are approved and used as anti-cancer therapeutics. Thus, discovery of new and potential HDAC inhibitors are necessary in the effective treatment of cancer. Materials and Methods: This study proposed a method using support vector machine (SVM) to classify HDAC8 inhibitors and non-inhibitors in early-phase virtual compound filtering and screening. The 100 experimentally known HDAC8 inhibitors including 52 inhibitors and 48 non-inhibitors were used in this study. A set of molecular descriptors was calculated for all compounds in the dataset using ADRIANA. Code of Molecular Networks. Different kernel functions available from SVM Tools of free support vector machine software and training and test sets of varying size were used in model generation and validation. Results and Conclusion: The best model obtained using kernel functions has shown 75% of accuracy on test set prediction. The other models have also displayed good prediction over the test set compounds. The results of this study can be used as simple and effective filters in the drug discovery process.

• The Korean Journal of Mycology
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• v.23 no.3 s.74
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• pp.275-283
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• 1995

The nutritional requirements of mycelial growth for Pleurotus spp. were studied. As the carbon sources, soluble starch and dextrin, nitrogen sources, arginine and ammonium tartrate, and calcium sources, $CaCO_3$ enhanced mycelial growth. Optimum C/N ratio was 100 : 1. On the base of results from the experiment on nutritional requirements, the following receipe is suggested for growth of Pleurotus spp.; starch 15 g, arginine 3.484 g, ammonium tartrate 3.06 g, $CaCO_3$ 0.314 g, $KH_2PO_4$ 8.138 g, $K_2HPO_4$ 1.584 g, $MgSO_4{\cdot}7H_2O$ 1.5 g for P. sajor-caju and 2.5 g for P. ostreatus. $FeSO_4{\cdot}7H_2O$ 0.02 g, $ZnSO_4{\cdot}7H_2O$ 0.03 g, $MnSO_4{\cdot}7H_2O$ 0.02 g, optimum pH 6.0. This new synthetic medium is tentatively designated as Park's medium.