• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.383-387
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• 2005

One of the most important issues in post-genome era is identifying functions of genes and understanding the interaction among them. Such interactions from complex biochemical pathways, which are very useful to understand the organism system. We present an integrated biochemical pathway database system with a set of software tools for reconstruction, visualization, and simulation of the pathways from the database. The novel features of the presented system include: (a) automatic integration of the heterogeneous biochemical pathway databases, (b) gene ontology for high quality of database in the integration and query (c) various biochemical simulations on the pathway database, (d) dynamic pathway reconstruction for the gene list or sequence data, (e) graphical tools which enable users to view the reconstructed pathways in a dynamic form, (f) importing/exporting SBML documents, a data exchange standard for systems biology.

• Journal of Convergence for Information Technology
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• v.10 no.3
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• pp.76-91
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• 2020

Whole genome sequence of Abeliophyllum distichum Nakai (Oleaceae) cultivar Ok Hwang 1 Ho, which is Korean endemic species, was recently sequenced to understand its characteristics. Acteoside is one of major useful compounds presenting various activities, and its several proposed biochemical pathways were reviewed and integrated to make precise biochemical pathway. Utilizing MetaPre-AI^TM which was developed for predicting secondary metabolites based on whole genome with the precise biochemical pathway of acteoside and the InfoBoss Pathway Database, we successfully rescued all enzymes involved in this pathway from the genome sequences, presenting that A. distichum cultivar Ok Hwang 1 Ho may produce acteoside. High-performance liquid chromatography result displayed that callus of A. distichum cultivar Ok Hwang 1 Ho contained acteoside as well as isoacteoside which may be derived from acteoside. Taken together, we successfully showed that MetaPre-AI^TM can predict secondary metabolite from plant whole genomes. In addition, this method will be efficient to predict secondary metabolites of many plant species because DNA can be analyzed more stability than chemical compounds.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.415-420
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• 2005

Mathematical modeling and simulation of biochemical reaction networks gained a lot of attention recently since it can provide valuable insights into the interrelationships and interactions of genes, proteins and metabolites in a reaction network. A number of attempts have been made for modeling and storing biochemical reaction networks without their dynamical properties but unfortunately storing and efficiently querying of the dynamic (mathematical) models are not yet studied extensively. In this paper, we present a novel nested relational data schema to store a pathway with its dynamic properties. We then show how to make the mapping between this dynamic pathway schema with the corresponding static pathway representation.

• Journal of KIISE:Databases
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• v.30 no.6
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• pp.573-584
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• 2003

Recent massive data generation by genomics and proteomics requires bioinformatic tools to extract the biological meaning from the massive results. Here we introduce ROSPath, a database system to deal with information on reactive oxygen species (ROS)-mediated cell signaling pathways. It provides a structured repository for handling pathway related data and tools for querying, displaying, and analyzing pathways. ROSPath data model provides the extensibility for representing incomplete knowledge and the accessibility for linking the existing biochemical databases via the Internet. For flexibility and efficient retrieval, hierarchically structured data model is defined by using the object-oriented model. There are two major data types in ROSPath data model: ‘bio entity’ and ‘interaction’. Bio entity represents a single biochemical entity: a protein or protein state involved in ROS cell-signaling pathways. Interaction, characterized by a list of inputs and outputs, describes various types of relationship among bio entities. Typical interactions are protein state transitions, chemical reactions, and protein-protein interactions. A complex network can be constructed from ROSPath data model and thus provides a foundation for describing and analyzing various biochemical processes.

• Journal of Microbiology and Biotechnology
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• v.19 no.1
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• pp.23-36
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• 2009

In the present work, the metabolic network of primary metabolism of the slow-growing myxobacterium Sorangium cellulosum was reconstructed from the annotated genome sequence of the type strain So ce56. During growth on glucose as the carbon source and asparagine as the nitrogen source, So ce56 showed a very low growth rate of $0.23\;d^{-1}$, equivalent to a doubling time of 3 days. Based on a complete stoichiometric and isotopomer model of the central metabolism, $^{13}C$ metabolic flux analysis was carried out for growth with glucose as carbon and asparagine as nitrogen sources. Normalized to the uptake flux for glucose (100%), cells recruited glycolysis (51%) and the pentose phosphate pathway (48%) as major catabolic pathways. The Entner-Doudoroff pathway and glyoxylate shunt were not active. A high flux through the TCA cycle (118%) enabled a strong formation of ATP, but cells revealed a rather low yield for biomass. Inspection of fluxes linked to energy metabolism revealed that S. cellulosum utilized only 10% of the ATP formed for growth, whereas 90% is required for maintenance. This explains the apparent discrepancy between the relatively low biomass yield and the high flux through the energy-delivering TCA cycle. The total flux of NADPH supply (216%) was higher than the demand for anabolism (156%), indicating additional reactions for balancing of NADPH. The cells further exhibited a highly active metabolic cycle, interconverting $C_3$ and $C_4$ metabolites of glycolysis and the TCA cycle. The present work provides the first insight into fluxes of the primary metabolism of myxobacteria, especially for future investigation on the supply of cofactors, building blocks, and energy in myxobacteria, producing natural compounds of biotechnological interest.

• Proceedings of the Korean Society of Life Science Conference
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• 2002.09a
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• pp.9-17
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• 2002

Renaturation of Lysozyme by size exclusion chromatography(SEC) to improve yield as well as the initial and final protein concentration has been studied in detail, Although urea decreases the rate of proteins refolding, it can suppress protein aggregation to sustain pathway of correct refolding at high protein concentration, and there existed an optimum urea concentration in renaturation buffer. Lysozyme was successfully refolded from initial protein concentration of up to 100mg/m1 by SEC, the yield was more than 40%. And the refolding of Interferon-${\gamma}$ was further investigated.

• Journal of Microbiology and Biotechnology
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• v.30 no.3
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• pp.398-403
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• 2020

Rhamnose is a naturally occurring deoxysugar present as a glycogenic component of plant and microbial natural products. A recombinant mutant Escherichia coli strain was developed by overexpressing genes involved in the TDP-ʟ-rhamnose biosynthesis pathway of different bacterial strains and Saccharothrix espanaensis rhamnosyl transferase to conjugate intrinsic cytosolic TDP-ʟ-rhamnose with anthraquinones supplemented exogenously. Among the five anthraquinones (alizarin, emodin, chrysazin, anthrarufin, and quinizarin) tested, quinizarin was biotransformed into a rhamoside derivative with the highest conversion ratio by whole cells of engineered E. coli. The quinizarin glycoside was identified by various chromatographic and spectroscopic analyses. The anti-proliferative property of the newly synthesized rhamnoside, quinizarin-4-O-α-ʟ-rhamnoside, was assayed in various cancer cells.

• KSBB Journal
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• v.19 no.6 s.89
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• pp.467-470
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• 2004

We have investigated the key parameters affecting ATP regeneration in a cell-free protein synthesis system derived from Escherichia coli. When glucose-6-phosphate was used as an energy source, the efficiency of ATP regeneration sharply responded to pH change of reaction mixture. In addition, both productivity and reproducibility of protein synthesis was substantially enhanced by introducing appropriate amount of NAD into the reaction mixture. As a result, through the activation of glycolytic pathway under an optimal pH, the batch cell-free system produced over $300\;{\mu}g$ of protein in a 1 mL reaction.

• Journal of Ginseng Research
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• v.17 no.2
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• pp.131-134
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• 1993

Panaxadiol (PD) from Korean red ginseng C.A. Meyer did not control the concentration of cytosolic free $Ca^{2+}$ influxes by thrombin (5 $\mu$/ml). However, PD strongly inhibited the synthesis of thromboxane. $A_2$ (TX$A_2$) in the aggregation of human platelets induced by thrombin (5 $\mu$/ml). These rexults suggest that PD blocks the any Pathway transforming to TX$A_2$ from arachidonic acid (AA) which release out of plasma membrane phospholipids by $Ca^{2+}$-dependent phospholipase C or phospholipase $A_2$. It may be also concluded that PD has the antiplatelet function by inhibiting the synthesis of TX$A_2$, which known to be the potent stimulator of the aggregation of human platelet.

• Journal of Microbiology and Biotechnology
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• v.26 no.5
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• pp.967-974
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• 2016

Zearalenone (ZEA) is an estrogenic mycotoxin that is produced by several Fusarium species, including Fusarium graminearum. One of the ZEA biosynthetic genes, ZEB2, encodes two isoforms of Zeb2 by alternative transcription, forming an activator (Zeb2L-Zeb2L homooligomer) and an inhibitor (Zeb2L-Zeb2S heterodimer) that directly regulate the ZEA biosynthetic genes in F. graminearum. Cyclic AMP-dependent protein kinase A (PKA) signaling regulates secondary metabolic processes in several filamentous fungi. In this study, we investigated the effects of the PKA signaling pathway on ZEA biosynthesis. Through functional analyses of PKA catalytic and regulatory subunits (CPKs and PKR), we found that the PKA pathway negatively regulates ZEA production. Genetic and biochemical evidence further demonstrated that the PKA pathway specifically represses ZEB2L transcription and also takes part in posttranscriptional regulation of ZEB2L during ZEA production. Our findings reveal the intriguing mechanism that the PKA pathway regulates secondary metabolite production by reprograming alternative transcription.