• Journal of Microbiology and Biotechnology
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• 제22권11호
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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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• 제41권4호
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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.

• 한국정보과학회논문지:컴퓨팅의 실제 및 레터
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• 제11권6호
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• pp.503-513
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• 2005

계산을 통한 단백질 상호작용 예측 기법의 중요성이 제기되면서 많은 단백질 상호 작용 예측 기법이 제안되고 있다. 하지만 이러한 기법들이 일반 사용자가 손쉽게 사용할 수 있는 서비스 형태로 제공되고 있는 경우는 드물다. 본 논문에서는 현재까지 알려진 단백질 상호작용 예측 기법 중 예측 기법의 완성도가 높고 상대적으로 예측 정확도가 높은 것으로 알려진 도메인 조합 기반 단백질 상호 작용 예측 기법을 이용하여 서비스 시스템으로 설계하고 구현하였다. 효모(Yeast)의 단백질 집합에 대하여 학습한 후, 학습된 단백질 집합과 공통된 도메인을 가지지만 학습 집합에 존재하지 않는 단백질 쌍들에 예측 기법을 적용하여 매우 높은 $77\%$의 민감도(sensitivity)와 $95\%$의 특이도(specificity)를 보였다. 더불어 DIP CORE, HMS-PCI, TAP 데이타의 테스트를 통해서 이 기법의 안정성을 확인하였다. 시스템의 기능들은 핵심 기능, 부가 기능 그리고 일반 서비스 기능으로 분류하였다. 시스템 설계의 주요 목표인 성능, 개방성 그리고 확장성에 따라, 개별 서비스들은 병렬화, 웹 서비스 표준 준수 및 계층화된 구조화를 지원하도록 구현하였다. 본 논문에서는 몇 가지 대표적인 사용자 인터페이스와 상세한 사용 지침도 소개한다.

• 한국근적외분광분석학회:학술대회논문집
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• 한국근적외분광분석학회 2001년도 NIR-2001
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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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• 제17권9호
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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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• 제어로봇시스템학회 2003년도 ICCAS
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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.

• 한국자기공명학회논문지
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• 제21권1호
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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.

• 한국콘텐츠학회논문지
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• 제9권5호
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• pp.332-336
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• 2009

유전체 분석에서 중요한 부분 중 하나는 기능이 알려지지 않은 미지 단백질에 대한 기능 예측이다. 단백질-단백질 상호작용 네트워크를 분석하는 것은 미지 단백질에 대한 기능을 보다 쉽게 예측할 수 있게 한다. 단백질-단백질 상호작용 네트워크로부터 미지 단백질의 기능을 예측하기 위한 다양한 연구들이 시도되어 왔다. 카이-제곱(Chi-square) 방식은 단백질-단백질 상호작용 네트워크를 통해 기능을 예측하고자 하는 연구 중 대표적인 방식이다. 하지만 카이-제곱 방식은 네트워크의 토폴로지를 반영하지 않아 네트워크 크기에 따라 예측의 정확성이 떨어지는 문제점이 있다. 따라서 본 논문에서는 카이-제곱 방식을 보완하여 정확성을 높인 새로운 기능 예측 방법을 제안한다 이를 위해 MIPS, DIP 그리고 SGD와 같은 공개된 단백질 상호작용 데이터베이스들로부터 데이터를 수집하여 분석하였다. 그리고 제안된 방식의 우수성을 입증하기 위해 각 데이터베이스들에 대해 카이-제곱방식과 제안하는 보완된 카이-제곱(Modified Chi-square)방식으로 예측해보고 이들의 정확성을 평가하였다.

• 한국식품과학회지
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• 제8권4호
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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.

• 한국동물학회지
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• 제31권3호
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• pp.157-164
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• 1988

SCK종양세포에 온열처리와 여러가지 sulihydryl-reacting agents을 처리하여 stress protein의 합성을 유도하고, 그 양상을 검토해 봄으로서 stress proteins의 합성유도와 denatured protein의 생성과의 관계를 고찰하였다. 세포에 cycloximid와 더불어 Zn또는 ME를 처리한 경우에는 stress protein의 합성이 일어나지 않았으나,온열처리 또는 IAA를 처리한 경우에는 stress protein의 합성이 유도되었다. 이 결과로 미루어 볼 때,stress protein의 유도 경로에는 두 가지가 있어서 새로운 단백질의 합성이 필요한 경로와 새로운 단백질의 합성과는 무관한 경로가 있는 것으로 추정할 수 있었다. 결국, 본 실험에서 사용한 stress들이 기존의 mature protein을 denature시키거나 (온열처리 또는 IAA),새로 합성된 immature protein을 denatur시키는 것,(Zn 또는 ME)으로 알려져 있으므로,stress에 의한 abnormal protein의 출현이 stress proteins의 합성을 유도하는 tigger의 구실을 하는 것으로 생각된다. 이 밖에 여러 가지 stress가 동시에 작용할 경우, 세포는 보다 강한 stress에 대해서 stress protein을 합성하여 대치하게 되는 것으로 생각된다.