• Journal of Microbiology and Biotechnology
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• v.22 no.11
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• pp.1575-1579
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• 2012

Paenibacillus polymyxa is known to be a plant-growth-promoting rhizobacterium. The present study describes a quantitative polymerase chain reaction (qPCR) assay for the specific detection and quantitation of P. polymyxa using a primer pair based on the sequence of a membrane-fusion protein for the amplification of a 268 bp DNA fragment. This study reports that the qPCR-based method is applicable for the rapid and sensitive detection of P. polymyxa and can be used as an alternative method for agricultural soil monitoring.

• Journal of Ginseng Research
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• v.41 no.4
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• pp.534-539
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• 2017

Background: Ginsenosides are the main ingredients of ginseng, which, in traditional Eastern medicine, has been claimed to have therapeutic values for many diseases. In order to verify the effects of ginseng that have been empirically observed, we utilized the reverse docking method to screen for target proteins that are linked to specific diseases. Methods: We constructed a target protein database including 1,078 proteins associated with various kinds of diseases, based on the Potential Drug Target Database, with an added list of kinase proteins. We screened 26 kinds of ginsenosides of this target protein database using docking. Results: We found four potential target proteins for ginsenosides, based on docking scores. Implications of these "hit" targets are discussed. From this screening, we also found four targets linked to possible side effects and toxicities, based on docking scores. Conclusion: Our method and results can be helpful for finding new targets and developing new drugs from natural products.

• Journal of KIISE:Computing Practices and Letters
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• v.11 no.6
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• pp.503-513
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• 2005

With the recognition of the importance of computational approach for protein-protein interaction prediction, many techniques have been developed to computationally predict protein-protein interactions. However, few techniques are actually implemented and announced in service form for general users to readily access and use the techniques. In this paper, we design and implement a protein interaction prediction service system based on the domain combination based protein-protein interaction prediction technique, which is known to show superior accuracy to other conventional computational protein-protein interaction prediction methods. In the prediction accuracy test of the method, high sensitivity($77\%$) and specificity($95\%$) are achieved for test protein pairs containing common domains with teaming sets of proteins in a Yeast. The stability of the method is also manifested through the testing over DIP CORE, HMS-PCI, and TAP data. Performance, openness and flexibility are the major design goals and they are achieved by adopting parallel execution techniques, web Services standards, and layered architecture respectively. In this paper, several representative user interfaces of the system are also introduced with comprehensive usage guides.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1616-1616
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• 2001

To select kernels for breeding that have required constituent content from either naturally distributed samples or artificially mutated ones, it is necessary to process batch samples in a short time. The constituent content of single-kernel grains such as wheat and rice has been determined using conventional bench type NIR instruments; however, it takes a lot of time and effort. Shizuoka Seiki (Fukuroi-city, Japan) and NFRI (National Food Research Institute) of MAFF (Ministry of Agriculture, forestry and Fisheries of Japan) have jointly developed a continuous high-speed single-kernel brown rice sorting machine based on rice protein content. It consists of several sections such as a feeding mechanism, measuring unit, sorting mechanism and controlling PC. The feeding mechanism picks up single-kernel brown rice from the hopper (maximum of 5kg storage capacity) and sends it to the measuring unit. A spectrum of the brown rice is obtained in the measuring unit, which consists of a near-infrared array sensor. The brown rice is then sorted in the sorting mechanism based on its protein content estimated by the controlling PC. In the present study, measuring speed was approximately 500ms for the full spectrum range and overall sorting speed was approximately 2.8s for one kernel. Accuracy of estimation was approximately SEP=0.5% of dry matter protein content for nonglutinous rice.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.9
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• pp.1296-1302
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• 2004

This study was conducted to evaluate the possible application of 2 D-SDS-PAGE (2 DE)-based proteome analysis techniques to the assessment of extreme proteolysis in postmortem skeletal muscle. Eight Hanwoo longissimus muscles were incubated immediately after slaughter for 24 h at 5$^{\circ}C$, 15$^{\circ}C$ or 36$^{\circ}C$. Warner Bratzler (WB)-shear force and ultrastructural configuration were determined at 24 h, and rate of proteolysis to 24 h was determined by 1 D-SDS-PAGE (1 DE) and 2 DE. In addition, tentative protein identification was performed from peptide mass fingerprints of MALDI-ToF analysis of major protein groups on 2 DE profiles. The result showed that although ultrastructural configuration was similar between the 5$^{\circ}C$ and 36$^{\circ}C$ treatments, meat at 5$^{\circ}C$ had higher WBshear force (approximately 5 kg greater). A higher rate of protein degradation at 36$^{\circ}C$ was observed based on Troponin-T degradation, 1 DE, and 2 DE analysis. This indicates that proteolysis during the early postmortem period was a significant determinant of shear force at 24 h. Little difference in proteolysis between 5$^{\circ}C$ and 15$^{\circ}C$ treatments was found based on classic 1 DE profile assessment. Meanwhile, considerable differences in the 2 DE profiles between the two treatments were revealed, with substantially higher rate of proteolysis at 15$^{\circ}C$ compared to 5$^{\circ}C$. Nuclease treatment improved 2 DE profile resolution. 400 ${\mu}$g and 600 ${\mu}$g of sample loading appeared to be appropriate for 24 cm pH 3-10 and pH 5-7 IPG strips, respectively. Protein detection and quantification of the 5$^{\circ}C$, 15$^{\circ}C$ and 36$^{\circ}C$ 2 DE profiles revealed 78, 163 and 232 protein spots respectively that were differentially modified in terms of their electrophoretic properties between approximately pI 5.3-7.7 with the molecular weight range of approximately 71-12 kDa. The current results demonstrated that 2 DE was a superior tool to 1 DE for characterising proteolysis in postmortem skeletal muscle.

• 제어로봇시스템학회:학술대회논문집
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• 2003.10a
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• pp.2356-2361
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• 2003

Proteome research in the medical field is expected to accelerate the understanding of disease mechanism, and to create new diagnostic concept. For protein profiling, this paper proposes a new methodology named CPDIB (Crude Protein Direct Blotting). In the CPDIB procedure, crude protein sample is directly immobilized on a membrane and the expression of protein molecules in the sample are analyzed quantitatively by using a special device called ImmobiChip, where the membrane is used as a field of the immune reaction. The over-all structure of the ImmobiChip is based on the conventional Slot blot device. Mechanical improvement in the air-tightness of the case holding the membrane realizes the direct blotting and results in high performance of stability in the immune reaction. In the measurement of multiple proteins, a dispensing robot is used for increasing the efficiency of handling of liquid. Cooperation of the dispensing robot with the ImmobiChip for immobilizing proteins realizes automated and stable performance of the CPDIB procedure. This paper shows the evaluation of the air-tightness of the ImmobiChip, the ability of analyzing proteins using the CPDIB procedure and the performance of the automated equipment.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.1
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• pp.13-19
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• 2017

Human sterol ${\Delta}8-{\Delta}7$ isomerase, commonly known as emopamil binding protein (EBP), is an essential protein in the cholesterol-synthetic pathway, and mutations of this protein are critically associated with human diseases such as Conradi-Hunermann-Happle or male EBP disorder with neurological defects syndrome. Due to such a clinical importance, EBP has been intensively investigated and some important features have been reported. EBP is a tetra-spanning membrane protein, of which $2^{nd}$, $3^{rd}$, and $4^{th}$ membrane-spanning ${\alpha}$ helices play an important role in its enzymatic function. However, detailed structural feature at atomic resolution has not yet been elucidated, due to characteristic difficulties in dealing with membrane protein. Here, we over-expressed EBP using Escherichia coli and performed detergent screening to find suitable membrane mimetics for structural studies of the protein by NMR. As results, DPC and LMPG could be evaluated as the most favorable detergents to acquire promising NMR spectra for structural study of EBP.

• The Journal of the Korea Contents Association
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• v.9 no.5
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• pp.332-336
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• 2009

Functional prediction of unannotated proteins is one of the most important tasks in yeast genomics. Analysis of a protein-protein interaction network leads to a better understanding of the functions of unannotated proteins. A number of researches have been performed for the functional prediction of unannotated proteins from a protein-protein interaction network. A chi-square method is one of the existing methods for the functional prediction of unannotated proteins from a protein-protein interaction network. But, the method does not consider the topology of network. In this paper, we propose a novel method that is able to predict specific molecular functions for unannotated proteins from a protein-protein interaction network. To do this, we investigated all protein interaction DBs of yeast in the public sites such as MIPS, DIP, and SGD. For the prediction of unannotated proteins, we employed a modified chi-square measure based on neighborhood counting and we assess the prediction accuracy of protein function from a protein-protein interaction network.

• Korean Journal of Food Science and Technology
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• v.8 no.4
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• pp.263-272
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• 1976

According to the intercombined review of chemical and biological investigation it has been noted that the metabolizable energy per gram dietary protein of mixed diet of daily intake patterned by Korean population has been found 3.4-3.6 Cal., which entails 10-12% level of the protein calorie percentage of total metabolizable energy, the biological value being fallen within the scope 63-73. The structure of dietary protein has revealed that the lysine and isoleucine were primary limiting amino acids and threonine secondary limiting as a general trend, however, it is assumed that the ultimate nutritional effect of dietary protein might be restricted uniformly among regions by the amount of lysine, since the lysine availability has been yielded as low as 72-82% level. As for the net protein utillization NPUst falls in the range of 52-62 and the NPUop 47-58. In either part the mountainous region has demonstrated lowest value and the urban area highest, these trend being obviously associated with the ratio of animal protein relative to the vegetable origin. The net dietary protein calorie percentage (NDpCal %) has been found within the range of 5-7 that may be capable of meeting the requirement for the maintenance of adult, though for the growth it is insufficient. Present level of total caloric intake would not influence on the fate of protein value of prevailing regional diet in terms of caloric restriction, since the present intake of food energy is higher than the lower limit of caloric intake that would impair the biological performance of dietary protein fed ad libitum basis. Based on the protein efficiency, the adequacy of current level of protein intake was analyzed in terms of utilizable protein, and it has been demonstrated that the 37.8g of utilizable protein in the fishery region and 38.2g in the mountainous region were bellow the FAO recommendation. Accordin to the hematological study it may be interpreted that the anemic symptoms of the mountainous region has some possibility of being related to the inferior status of dietary protein in quality as well as in quantity.

• The Korean Journal of Zoology
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• v.31 no.3
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• pp.157-164
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• 1988

SCK tumor cells were exposed to heat shock or several sulihydryl-reacting agents such as iodoacetamide(IAA), zinc chloride(Zn), and 2-mercaptoethanol(ME). Stress proteins induced by these agents were examined and the relationship between the induction of stress proteins and the production of abnormal proteins was discussed. Based on the present experiments, two classes of intracellular pathways for the induction of stress proteins were defined; one dependent on and the other independent of protein synthesis. The presence of cycloheximide during the induction period blocked the formation of stress proteins in the cells exposed to Zn or ME, but not in those exposed to heat shock or IAA.Therefore, stress protein seems to be induced either by denaturation of pre-existing mature proteins (e.g., heat shock or IAA) or by newly synthesized abnormal proteins(e.g., Zn or ME). In conclusion, it is ilkely that the production of abnormal proteins by stresses triggers stress protein induction. In addition, it was found that the cells exposed to IISP and GRP inducers simultaneously responded to more strong stress among several stresses encountered.