• Journal of Ginseng Research
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• v.47 no.5
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• pp.662-671
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• 2023

Background: 20(S)-protopanaxadiol (PPD), a ginsenoside metabolite, has prominent benefits for the central nervous system, especially in improving learning and memory. However, its transcriptional targets in brain tissue remain unknown. Methods: In this study, we first used mass spectrometry-based drug affinity responsive target stability (DARTS) to identify the potential proteins of ginsenosides and intersected them with the transcription factor library. Second, the transcription factor PURA was confirmed as a target of PPD by biolayer interferometry (BLI) and molecular docking. Next, the effect of PPD on the transcriptional levels of target genes of PURA in brain tissues was determined by qRT-PCR. Finally, bioinformatics analysis was used to analyze the potential biological features of these target proteins. Results: The results showed three overlapping transcription factors between the proteomics of DARTS and transcription factor library. BLI analysis further showed that PPD had a higher direct interaction with PURA than parent ginsenosides. Subsequently, BLI kinetic analysis, molecular docking, and mutations in key amino acids of PURA indicated that PPD specifically bound to PURA. The results of qRT-PCR showed that PPD could increase the transcription levels of PURA target genes in brain. Finally, bioinformatics analysis showed that these target proteins were involved in learning and memory function. Conclusion: The above-mentioned findings indicate that PURA is a transcription target of PPD in brain, and PPD upregulate the transcription levels of target genes related to cognitive dysfunction by binding PURA, which could provide a chemical and biological basis for the study of treating cognitive impairment by targeting PURA.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.88-92
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• 2005

Aptamer is the single-stranded oligonucleotide which binds to various target molecules such as proteins, peptides, lipids and small organic molecules with high affinity and specificity. DNA aptamers specific for the $17{\beta}-estradiol$ were selected by SELEX (Systematic Evolution of Ligands by EXponential enrichment) process from a random DNA library. These DNA aptamers have a high affinity to $17{\beta}-estradiol$ as an endocrine disrupting chemical. Nanowell and $200{\mu}m$ gold electrode were used as substrate for DNA aptamer immobilization and electrochemical analysis. Especially, nanowell gold electrode was fabricated by e-beam lithography. The size of single nanowell is 130nm and 40,000 nanowells were deposited on one gold electrode. The immobilization method was based on the interaction between the biotinylated aptamer and streptavidin deposited on gold electrode previously. Immobilization procedure was optimized by surface plasma resonance (SPR) and electrochemical analysis. After the immobilization of DNA aptamer on streptavidin modified gold electrode, $17{\beta}-estradiol$ solution was treated on aptamer immobilized gold electrode. The current of gold electrode was decreased by the binding of $17{\beta}-estradiol$ to DNA aptamer immobilized on gold electrode. However, in negative control experiments of 1-aminoanthraquinone and 2-methoxynaphthalene, the current was rarely decreased. And more sensitive data was obtained from nanowell gold electrode comparing with $200{\mu}m$ gold electrode.

• Korean Journal of Plant Tissue Culture
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• v.27 no.4
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• pp.259-268
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• 2000

Senescence is a sequence of biochemical and physiological events that lead to death of a cell, organ, or whole organism. Senescence is now clearly regarded as a genetically determined and evolutionarilly acquired developmental process comprising the final stage of development. However, in spite of the biological and practical importance, genetic mechanism of senescence has been very limited. Through forward and reverse genetic approaches, we are trying to reveal the molecular and genetic mechanism of senescence in plants, employing leaf organs of Arabidopsis as a model system. Using forward genetic approach, we have initially isolated several delayed senescence mutants either from T-DNA insertional lines or chemical-mutagenized lines. In the case of ore 4 and ore 9 mutants, the mutated genes were identified. The recent progress on characterization of mutants and identification of the mutated genes will be reported. We are also screening mutations from other various sources of mutant pools, such as activation tagging lines and promoter trap lines. Two dominant senescence-delayed mutants were isolated from the activation tagging pool. Cloning of the genes responsible for this phenotype is in progress. For reverse genetic approach, the genes that induced during leaf senescence were first isolated by differential screening method. We are currently using PCR-based suppression subtractive hybridization, designed to enrich a cDNA library for rare differentially expressed transcripts. Using this method, we have identified over 35 new sequences that are upregulated at leaf senescence stage. We are investigating the function of these novel genes by systemically generating antisense lines.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1994.04a
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• pp.261-261
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• 1994

Bovine milk xanthine oxidase (E.C.1.1.3.22, XO) purchased from Sigma Chemical Co. had the three protein fragments below 150 kDa on 7.5％ SDS-PAGE, which did not show enzyme activity. To remove these fragments, the enzyme preparation was further purified through Sephadex G-200 column chromatography. Two peaks exhibiting enzymatic activity were separated very closely to the void volume, which were revealed as two different enzyme forms, dimeric and monomeric, confirmed by activity staining on native PAGE. Anti sera-against each of the two enzyme forms were raised by subcutaneous injection at multiple sites on the back of rabbits during 4 weeks. On the immunodiffusion test, it was found that both of the antisera of the two forms could react with each other, which implied that their epitopes were identical In the Western blot analysis of mouse liver cytosol fraction, it was found that rabbit anti-XO antibody bound well with the protein band of monomeric mouse liver XO of about 150kDa. Based on this result, mouse liver cDNA 1 ibrary was screened by in situ hybridizat ion wi th rabbi t anti -XO antibody as probe. Through the immunological screening, recombinant phages giving positive signal by the production of XO were selected and further purified. To validate these clones, purified phages were lysogenized in E. coli Y1089 and their lysates were analysed for enzyme activity and immunoreactivity, It was verified that lysates of the purified recombinant phage lysogens exhibited the enzymatic activity as well as bound wi th XO antibody, when induced by IPTG. The above results assert that selected recombinant phage carries mouse liver XO gene.

• Korean Journal of Pharmacognosy
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• v.40 no.4
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• pp.303-308
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• 2009

Essential oils of the musk from wild muskrat (Ondatra zibethicus) were analyzed by gas chromatography/mass spectrometry. Fifty-six chemical components were separated, and 14 volatile compounds (78% of composition of total essential oil) of macrocyclic musk, mainly cyclopentadecanone, 12-hydroxy-14-methyl-oxa-cyclotetradec-6-en-2-one, cycloheptadecanone and 9-cycloheptadecen-1-one, were identified by the comparison of Wiley/NBS Library from the results of GC-MS. However, l-muscone, a compound reported by earlier workers in the musk from muskrat, was not detected using the spike test in this study. Interestingly, cyclohexadecanone, which has the same molecular weight (Mw 238) as l-muscone, was identified. In addition, it is considered that because of possessing much higher amounts of macrocyclic components compared to the original musk, muskrat has higher economic values in perfume and pharmaceutical industries.

• Journal of Microbiology and Biotechnology
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• v.19 no.10
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• pp.1077-1084
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• 2009

A genomic library was constructed to clone a xylanase gene (Mxyn10) from Demequina sp. JK4 isolated from a deep sea. Mxyn10 encoded a 471 residue protein with a calculated molecular mass of 49 kDa. This protein showed the highest sequence identity (70%) with the xylanase from Streptomyces lividans. Mxyn10 contains a catalytic domain that belongs to the glycoside hydrolase family 10 (GH10) and a carbohydrate-binding module (CBM) belonging to family 2. The optimum pH and temperature for enzymatic activity were pH 5.5 and $55^{\circ}C$, respectively. Mxyn10 exhibited good pH stability, remaining stable after treatment with buffers ranging from pH 3.5 to 10.0. The protein was not significantly affected by a variety of chemical reagents, including some compounds that usually inhibit the activity of other related enzymes. In addition, Mxyn10 showed activity on cellulose. These properties mark Mxyn10 as a potential enzyme for industrial application and saccharification processes essential for bioethanol production.

• KSBB Journal
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• v.28 no.5
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• pp.295-302
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• 2013

Indigo is utilized in various industries including textile dyeing, cosmetics, printing and medicinal products and its reduced form, leuco-indigo, is mainly used in these process. Chemical reducing agent (sodium dithionite, sodium sulfide, etc.) is preferred to use for the formation of leucoindigo in industry. In traditional indigo fermentation process, microorganisms can participate in the reduction of indigo and thus it has been known to reduce environmental pollution and noxious byproducts. However, in fermentation method using microorganisms it is difficult to standardize large scale production process due to low yield and reproducibility. In this study, we attempted to develop the indigo reduction process using microbial flora which was isolated from naturally fermented indigo vat or deduced by metagenomic approach. From the results of library analyses of PCR-amplified 16S rRNA genes from the traditional indigo fermentation vat sample (metagenome), it was confirmed that Alkalibacteriums (71%) was distinctly dominant in population. Some strains were identified after confirming that they become pure culture in nutrient media modified slightly. Four strains were separated in this process and each strain showed obvious reducing ability toward indigo in dyeing test. It is expected that the analyzed results will provide important data for standardizing the natural fermentation of indigo and investigating the mechanism of indigo reduction.

• The Korean Journal of Food And Nutrition
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• v.32 no.6
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• pp.717-729
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• 2019

The chemical informs about 70 individual phenolic compounds were constructed from various lettuce samples based on literature sources and analytical data. A total of 30 phenolic compounds including quercetin 3-O-glucuronide, quercetin 3-O-(6''-O- malonyl) glucoside, cyanidin 3-O-(6''-O-malonyl)glucoside, chlorogenic acid and chicoric acid as major components were identified in 6 lettuce samples from Korea using UPLC-DAD-QToF/MS on the basis of constructed library. Among these, quercetin 3,7-di-O-glucoside(m/z 627 [M+H]⁺), quercetin 3-O-(2''-O-malonyl)glucoside(morkotin C, m/z 551 [M+H]⁺), quercetin 3-O-(6''- O-malonyl)glucoside methyl ester(m/z 565 [M+H]⁺), 5-O-cis-p-coumaroylquinic acid(m/z 339 [M+H]⁺) and 5-O-caffeoylquinic acid methyl ester(m/z 369 [M+H]⁺) were newly confirmed from the lettuce samples. In total content of phenolic compounds, 4 red lettuce samples(2,947.7~7,535.6 mg/100 g, dry weight) showed higher than green lettuce(2,687.3 mg) and head lettuce(320.1 mg).

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.18
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• pp.7785-7792
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• 2014

Background: Valproic acid (VPA) is a potent anticancer and antiangiogenic agent. However, design and synthesis of chemical derivatives with improved antiangiogenic and anticancer activities are still necessary. In this study a library of novel derivatives of VPA was synthesized and tested. Methods: A human liver cancer cell line (HepG2) and a human normal embryonic kidney cell line (HEK 293) were exposed to various concentrations of VPA derivatives for 24 hours and cell viability was checked by MTT colorimetric assay. Anti-angiogenic properties were evaluated in transgenic zebrafish embryos. Results: N-valproylglycine derivatives suppressed survival almost 70% (p value 0.001) in HepG2 cells but only 10-12% in HEK 293 cells (p value 0.133). They also suppressed angiogenic blood vessel formation by 80% when used between $2-20{\mu}M$ in zebrafish embryos. Valproic acid hydrazides showed moderate level of anticancer activity by affecting 30-50% (p value 0.001) of cell viability in HepG2 cells and 8-10% in HEK293 cells (p value 0.034). Conclusion: The majority of compounds in this study showed potent and stronger antiangiogenic and anticancer activity than VPA. They proved selectively toxic to cancer cells and safer for normal cells. Moreover, these compounds inhibited developmental angiogenesis in zebrafish embryos. Based on the fact that liver is a highly vascularized organ, in case of liver carcinoma these compounds have the potential to target the pathological angiogenesis and could be an effective strategy to treat hepatocellular carcinoma.

• Proceedings of the Korean Environmental Sciences Society Conference
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• 2003.11a
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• pp.73-78
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• 2003

In this research, we implement Realtime Air Diffusion Prediction System which is a parallel Fortran model running on distributed-memory parallel computers. The system is designed for air diffusion simulations with four-dimensional data assimilation. For regional air quality forecasting a series of dynamic downscaling technique is adopted using the NCAR/Penn. State MM5 model which is an atmospheric model. The realtime initial data have been provided daily from the KMA (Korean Meteorological Administration) global spectral model output. It takes huge resources of computation to get 24 hour air quality forecast with this four step dynamic downscaling (27km, 9km, 3km, and lkm). Parallel implementation of the realtime system is imperative to achieve increased throughput since the realtime system have to be performed which correct timing behavior and the sequential code requires a large amount of CPU time for typical simulations. The parallel system uses MPI (Message Passing Interface), a standard library to support high-level routines for message passing. We validate the parallel model by comparing it with the sequential model. For realtime running, we implement a cluster computer which is a distributed-memory parallel computer that links high-performance PCs with high-speed interconnection networks. We use 32 2-CPU nodes and a Myrinet network for the cluster. Since cluster computers more cost effective than conventional distributed parallel computers, we can build a dedicated realtime computer. The system also includes web based Gill (Graphic User Interface) for convenient system management and performance monitoring so that end-users can restart the system easily when the system faults. Performance of the parallel model is analyzed by comparing its execution time with the sequential model, and by calculating communication overhead and load imbalance, which are common problems in parallel processing. Performance analysis is carried out on our cluster which has 32 2-CPU nodes.