• Proceedings of the Korea Information Processing Society Conference
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• 2010.11a
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• pp.1834-1836
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• 2010

프로테오믹스는 세포 안 또는 개체 안의 모든 단백질을 총체적으로 연구하는 분야이다. 단백질 동정은 단백질이 어떤 아미노산의 서열로 구성되었는지를 확인하는 것이다. 하지만 Post-translational modification과 같은 단백질 변형을 고려하게 되면 단백질 동정은 매우 어렵게 된다. $MOD^i$ 알고리즘은 단백질 동정을 할 때 Post-translational modification의 종류나 개수에 제한 없이 단백질 동정을 정확하게 수행한다. 하지만, 대용량 단백질 서열 데이터베이스를 사용하면 수행시간이 많이 걸리는 단점이 있다. 본 논문에서는 $MOD^i$를 보완하기 위해 대용량 데이터베이스에서 후보 단백질을 선정하는 알고리즘을 통해서 개선된 $MOD^f$ 알고리즘을 제안하고 Target-decoy search strategy를 적용하여 정확성을 분석한다. 후보 단백질 선정 알고리즘과 Target-decoy search strategy 적용 결과 $MOD^f$는 $MOD^i$에 비해 정확도를 희생하지 않으면서 수행속도는 약 2배 향상되었다.

• Journal of The Korean Society of Grassland and Forage Science
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• v.31 no.2
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• pp.99-106
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• 2011

In order to investigate rice stem proteome in response to heat stress, rice plants were subjected to heat treatment at 42$^{\circ}C$ and total soluble proteins were extracted from stem tissues, and were fractionated with 15% PEG (poly ethylene glycol) and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE). After staining of 2-DE gels, 46 of differentially expressed proteins were extracted, digested by trypsin, and subjected to matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. Proteins were identified through database search by using peptide mass fingerprints. Among them, 10 proteins were successfully identified. Seven proteins were up- and 3 proteins were down-regulated, respectively. These proteins are involved in energy and metabolism, redox homeostasis, and mitochondrial small heat shock proteins. The identification of some novel proteins in the heat stress response provides new insights that can lead to a better understanding of the molecular basis of heat-sensitivity in plants, and also useful to molecular breeding of thermotolerant forage crops.

• Applied Biological Chemistry
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• v.36 no.6
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• pp.533-538
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• 1993

The Wx protein, known as starch synthase or starch glucosyl transferase (E.C. 2.4.1.11), is responsible for the amylose synthesis. In an effort to explain the mechanism of amylose biosynthesis, the starch synthase known as Wx protein was identified by analyzing the various wx rice mutants with SDS-PAGE of proteins extracted from rice starch. Finally, the 66 kDa protein was purified by extracting the starch-bound protein fractions followed by Suprose 12 gel filtration chromatography.

• Korean Journal of Environmental Agriculture
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• v.32 no.1
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• pp.48-54
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• 2013

BACKGROUND: Sorghum (Sorghum bicolor (L.) Moench) ranks as the 6th most planted crop in the world behind wheat, rice, maize, soybean, and barley. The objective of this study was to identify bio-marker among sorghum cultivars using proteomics approach such as two-dimensional polyacrylamide gel electrophoresis (2-DE) coupled with mass spectrometry (MS). METHODS AND RESULTS: Proteins were extracted from sorghum seed, and separated by 2-DE. Total 652 spots were detected from 4 different sorghum seed after staining of 2-DE with colloidal Coomassie brilliant blue (CBB). Among them, 8 spots were differentially expressed and were identified using MALDI-TOF/TOF mass spectrometry. They were involved in RNA metabolism (spot1, spot 4), heat shock proteins (HSPs, spot 2), storage proteins (spot 3, spot 5, and spot 6), and redox related proteins (spot 8). Eight of these proteins were highly up-regulated in Whinchalsusu (WCS). The HSPs, Cupin family protein, and Globulin were specifically accumulated in WCS. The DEAD-box helicase was expressed in 3 cultivars except for WCS. Ribonuclease T2 and aldo-keto reductase were only expressed in 3 cultivars except for Daepung-susu (DPS). CONCLUSION(S): Functions of identified proteins were mainly involved in RNA metabolism, heat shock protein (HSP), and redox related protein. Thus, they may provide new insight into a better understanding of the charactreization between the cultivars of sorghum.

• Korean Journal of Food Science and Technology
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• v.20 no.1
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• pp.90-94
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• 1988

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunodiffusion method were used for the species differentiation of yeasts, Saccharomyces cerevisiae, Candida utils, Candida tropicalis, and Kleuyveromyces fragilis. Comparing the electrophoretic patterns of soluble and membrane proteins, Saccharomyces cereνisiae was similar to Candida utilis but was different from Candida tropicalis and Kleuyveromyces fragilis. In immunochemical properties of soluble proteins, Saccharomyces cerevisiae was almost identical with Candido utilis. However, Saccharomyces cerevisiae or Candida utilis was quite different from Candida tropicalis and Kleuyveromyces fragilis in their immunoreactivities. In immunochemical properties of membrane proteins, almost the same results were obtained irrespective of four yeast species. By using SDS-PAGE and immunodiffusion methods, Saccharomyces cerevisiae and Candida utilis were difficult to differentiate but both species were easily differentiated from Candida tropicalis and Kleuyveromyces fragilis.

• Clinical and Experimental Pediatrics
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• v.52 no.5
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• pp.567-575
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• 2009

Purpose : Epilepsy affects more than 0.5% of the world's population. It has a large genetic component and is caused by electrical hyperexcitability in the central nervous system. Despite its prevalence, the disease lacks definitive diagnostic serological biomarkers. To identify potential biomarkers for epilepsy by a convenient method, we analyzed the expression of serum proteins, reflecting alterations in the patient's proteomes. Methods : We compared two-dimensional electrophoretic band patterns of human sera from eight patients with temporal lobe epilepsy (TLE) with those of eight control subjects. The differentially expressed bands were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and electrospray ionization quadrupole time-of-flight mass spectrometry. esults : Twelve proteins were differentially expressed in the TLE group, of which 6 were identified. Expression of haptoglobin Hp2, PRO2675, immunoglobulin heavy chain constant region gamma 2, an unnamed protein, and three unidentified proteins were upregulated in serum from the patients with TLE, whereas those of major histocompatibility complex (MHC) class I antigen, plasma retinol-binding protein precursor, and three unidentified proteins were downregulated in these patients. After resection of the epileptogenic zone, the expressions of MHC class I antigen, immunoglobulin heavy chain constant region gamma 2, two of the downregulated unidentified proteins, and one of the upregulated unidentified proteins returned to the normal range. Conclusion : The 12 serum proteins in this study are potentially useful biomarkers for the diagnosis and monitoring of TLE.

• Journal of The Korean Society of Grassland and Forage Science
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• v.25 no.4
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• pp.287-296
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• 2005

To investigation protein expression pattern in rice leaves exposed to cold stress, the soluble proteins extracted from leaf tissue were fractionated with $15\%$ PEG and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE). Differentially expressed proteins were identified by peptide mass fingerprinting using matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Eight proteins up-regulated and 10 down-regulated were found in $15\%$ PEG supernatant fraction. In addition, 13 proteins up-regulated and 14 down-regulated were found in $15\%$ PEG pellet fraction. It was identified the differentially expressed proteins in $15\%$ PEG supernatant fraction as pimerase/dehydratase fructokinase, ribose-5-phosphate isomerase (Rpi), chaperonin 21 precursor, probable photosystem II oxygen-envolving complex (PS II OEC) protein 2 precursor and thioredoxin h-type (Trx-h) and those in $15\%$ PEG pellet fraction as OSINBb0059K02.15, hypothetical protein, putative mitogen-activated protein kinase kinase (MAPKK), beta 7 subunit of 205 proteasome, ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit. These proteins are involved in metabolism, energy, protein synthesis, disease/defense and signal transduction-related proteins.

• Environmental Analysis Health and Toxicology
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• v.22 no.4
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• pp.305-312
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• 2007

환경오염을 신속하게 모니터링하기 위한 생물지표의 개발은 증가하고 있는 오염의 심각성에 비추어 매우 중요한 과제로 여겨지고 있다. 본 연구에서는 독성물질처리에 의하여 선택적으로 발현이 조절되는 단백질의 동정을 통하여 독성물질에 대한 단백질 생물지표를 발굴하고자 시도하였다. 즉, 송사리(Oryzias latipes)를 유기인계 살충제인 다이아지논(diazinon)에 0, 0.1, 1, 5 mg/L 농도로 24시간 노출시킨 후, 머리와 몸통부분으로 나누어 단백질 발현패턴을 분석하였다. 본 시스템에서 다이아지논 처리에 의하여 유의적으로 발현이 증가된 단백질로서 alpha-tubulin, ribonuclease pancreatic precursor, protein hfq 등을 동정하였으며, 이 가운데 alpha-tubulin과 $hsp90{\beta}$의 발현이 다이아지논 농도에 의존적으로 증가하는 것을 semi-quantitative RT-PCR방법으로 확인하였다. 이와 같이 다이아지논 처리에 특이적으로 발현이 증가된 송사리 단백질들은 노출평가를 위한 생물지표로서 개발에 응용될 수 있을 것으로 평가된다.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.10 no.6
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• pp.1407-1413
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• 2009

The present study was conducted to gain insights into oocyte maturation and early embryo development, SELDI-TOF-MS was used to find the protein candidates that are specifically or prominently expressed in mouse oocytes at the in vitro matured metaphase II (MIl) and germinal vesicle (GV) stages. By using selected CM10 chip, found 16 candidates which were up-regulated in GV stage oocytes compared with in MIl stage oocytes, molecular weight are 8180 (2 candidates), 10226 (5 candidates), 15767 (5 candidates) and 16770 (4 candidates) Da respectively. And 29 candidates were higher in MIl than in GV stage oocytes, molecular weight are 10832 (3 candidates), 17744(8 candidates), 20122 (3 candidates), 22131 (3 candidates), 24857 (7 candidates) and 33507 (5 candidates) Da, respectively. All (45) candidate (0.2 and 1.0 % error tolerances) were performed real time RT-PCR analysis and further selected 13 more potential candidates.

• Journal of Korean Society of Environmental Engineers
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• v.36 no.4
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• pp.265-270
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• 2014

Protease producing microorganisms were isolated from many kinds of food waste and fermented foods, which contains high amount and variable kinds of degraded substances. Several microorganisms were identified by 16S rRNA full sequencing analysis methods. The activity of protease was analyzed and identified in variable conditions for the application. For industrial use for biowaste treatment some proteases were isolated, identified and selected from microbial cells. And the tests were carried for the further use. The protein degrading activity at low temperature is useful for the treatment of organic waste, which contains much proteins. By the protein degradation process the organic waste can be utilized in variable fields, for example from feedstuff supplement to fertilizer for agriculture. Bacterial cells with protease activity at low temperature were isolated and identified. The optimal conditions for microbial cultivation and protease production were studied.