• Genomics & Informatics
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• v.9 no.4
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• pp.197-199
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• 2011

The biological interpretation of two-dimensional (2D) gel electrophoresis experiments is a key step toward understanding the functions of biological systems. We here present a web-based integrated database, called 2DSpotDB, for the management of proteome data derived from several pathogens. The 2DSpotDB was established as a part of the management of a pathogen proteome project at the Korea National Institute of Health. The goals of the 2DSpotDB implementation are to store and define important pathogen genes, retrieve information obtained by 2D polyacrylamide gel electrophoresis and mass spectrometry, and create an integrated system to provide pathogen proteome information for biological scientists. This database currently contains 14 gels and information on 387 protein spots, among which 329 proteins were identified and annotated.

• 한국생물공학회:학술대회논문집
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• 2003.10a
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• pp.746-749
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• 2003

Alignment of 2D-gel images of biological samples can visualize the difference of expression profiles and also inform us candidates of protein spots to be further analyzed. However, comparison of two proteome images between case and control does not always successfully identify differentially expressed proteins due to sample-to-sample variation. Because of poor reproducibility of 2D-gel electrophoresis, sample-by-sample variations and inconsistent electrophoresis conditions, multiple number of 2D-gel image must be processed to align each other to visualize the difference of expression profiles and to deduce the protein spots differentially expressed with reliability. Alignment of multiple 2D-Gel images and their clustering were carried out by applying various algorithms and statistical methods. In order to align multiple images, multiresolution-multilevel algorithm was found out to be suitable for fast alignment and for distorted images. Clustering of 12 different images implementing a k-means algorithm gives a phylogenetic tree of distance map of the proteomes. Microsoft Visual C++ was used to implement the algorithms in this work.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.222-227
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• 2018

Mycobacterium tuberculosis (MTB)-originated lipid antigen is presented on the antigen-presenting cell surface with CD1b. When monocyte-derived dendritic cells phagocytosed MTB H37Rv (Multiplicity of infection 10, infectivity: 46.89%), the CD1b expression level decreased slowly. Since this was just a live MTB-mediated phenomenon, it was not detected from heat-killed MTB or mycolic acid, which is a unique antigen of MTB. We confirmed that the phosphorylation of CD1b molecules using 2D electrophoresis with staining could phosphorylate and induce the presentation of the lipid antigen using the phagocytosis assay.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.58 no.4
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• pp.388-392
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• 2013

The proteins from functional rice cultivars (Nogwonchalbyeo, Giant embryonic, Arhyangchalbyeo, and Goamibyeo) and general white rice were extracted and separated using two-dimensional (2D) gel electrophoresis. A wide variation in the molecular weight (MW) and pH range of the expressed proteins in rice samples were observed. The green-kerneled rice (Nogwonchalbyeo) exhibited proteins with MW of 9-57 kDa and appeared at a pH range of 4-7. The Giant embryonic contained proteins with MW of 31-63 kDa and a pH range of 5-6. The aromatic glutinous rice (Arhyangchalbyeo) showed proteins with MW of 24-28 and pH of 5.8-6.8. The high-amylose rice (Goamibyeo) exhibited proteins with MW of 3-63 and pH of 5.2-5.6. The identified proteins uniquely found and highly expressed in each cultivar may have a significant role on rice functionality. The results illustrate that the 2D gel electrophoresis is a valuable method in the determination of the protein expression profiles in functional rice grains and may be useful in the identification of specific marker proteins associated with the functional property of rice.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.788-795
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• 2015

Two dimensional-fluorescence difference gel electrophoresis (2D DIGE) is an emerging technique for comparative proteomics, which improves the reproducibility and reliability of differential protein expression analysis between samples. The purpose of this study was to investigate bovine pregnancy-specific proteins in the proteome between bovine pregnant and non-pregnant serum using DIGE technique. Serums of 2 pregnant Holstein dairy cattle at day 21 after artificial insemination and those of 2 non-pregnant were used in this study. The pre-electrophoretic labeling of pregnant and non-pregnant serum proteins were mixed with Cy3 and Cy5 fluorescent dyes, respectively, and an internal standard was labeled with Cy2. Labeled proteins with Cy2, Cy3, and Cy5 were separated together in a single gel, and then were detected by fluorescence image analyzer. The 2D DIGE method using fluorescence CyDye DIGE flour had higher sensitivity than conventional 2D gel electrophoresis, and showed reproducible results. Approximately 1,500 protein spots were detected by 2D DIGE. Several proteins showed a more than 1.5-fold up and down regulation between non-pregnant and pregnant serum proteins. The differentially expressed proteins were identified by MALDI-TOF mass spectrometer. A total 16 protein spots were detected to regulate differentially in the pregnant serum, among which 7 spots were up-regulated proteins such as conglutinin precursor, modified bovine fibrinogen and IgG1, and 6 spots were down-regulated proteins such as hemoglobin, complement component 3, bovine fibrinogen and IgG2a three spots were not identified. The identified proteins demonstrate that early pregnant bovine serum may have several pregnancy-specific proteins, and these could be a valuable information for the development of pregnancy-diagnostic markers in early pregnancy bovine serum.

• International Journal of Industrial Entomology and Biomaterials
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• v.17 no.2
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• pp.217-221
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• 2008

Dung beetle larvae at the $3^{rd}$ instar were injected with lipopolysaccaride and inducible proteins were examined within a pI level of 3-10 and a size level by proteomics, including 1-D SDS PAGE analysis and antibacterial assay. The immune infected larvae extracts provided seven protein bands in one-dimensional electrophoresis and its antibacterial activity also checked. Hemolymph protein from immune infected larvae of the dung beetle were separated by twodimensional gel electrophoresis and compared with those from native larvae. In 2-D gel electrophoresis, we detected 63 immune infected unique and 32 up-regulated proteins, and 36 proteins that were down-regulated or not present in treated gel. Ten protein spots from unique proteins and those presented as different level of abundance in infected and native larvae were specially expressed. These differentially expressed proteins were proposed to be involved in the defense mechanism against microorganism.

• Journal of Life Science
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• v.12 no.2
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• pp.208-212
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• 2002

Human $\varepsilon$-globin DNA fragment was used to determine the thermal stabilities of base pairs at d(CXG) and d(GXC) by Temperature Gradient Gel Electrophoresis(TGGE). The base pair stability depends on the hydrogen bonding interaction and base stacking interaction of neighbor base sequence. The orders of base pair stabilities were T.AG.A = A.G>C.T>T.C>C.A>A.C for d(GXC).d(GYC).

• Korean Journal of Microbiology
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• v.27 no.1
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• pp.35-42
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• 1989

The mode of transglycosylation reaction observed during the action of low-molecular-weigh $\beta$-D-glucosidase ($\beta$-D-glucoside glucohydrolase, EC3.2.1.21) purified from Trichoderma koningii ATCC 26113 was investigated using $^{1}H$-NMR spectroscopy. The enzyme was purified by the series of procedures including ammonium sulfate precipitation, and fractionations by column chromatographies on Bio-Gel P-150, DEAE-Sephadex A-50, and SP-Sephadex C-50. The final purification was performed by the band eluation after preparative polyacrylamide gel electrophoresis. The enzyme showed its molecular size of 78,000 through the analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and its isoelectric point of 5.80 through the analysis of analytical isoelectric focusing. The H-1 proton resonances were analyzed. After the reaction of the enzyme with cellobiose, the reaction products were separated by high performance liquid chromatography using refractive index detector. H-1 resonances of the products were consisted with those of gentiobiose [$\beta$-D-glucopyranosyl--(1,6)-D-glucopyranose], and cellotriose [$\beta$-D glucopyranosyl-(1,4)-$\beta$-D-glucopyranosyl]-(1,4)-D-glucopyranose] with minor resonances of sophorose [$\beta$-D-glucopyranosyl-(1,2)-D-glucopyranose], respectively.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.50 no.spc1
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• pp.4-7
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• 2005

The pharmaceutical function of tocotrienol in rice bran was evaluated. Distinctive antioxidative effects by 1,1-diphenyl-2-picrylhydrazyl(DPPH) could be observed. Also, Superoxide Dismutase(SOD) and Glutathione Peroxidase(GPX) activities of the cultured cells such as human firbroblast and hepatocyte, were increased up to 2 fold by the treatment of tocotrienol. The effects on GPX activity were more evident than SOD activity, and the stimulation was up to 2 fold. The changes of gene expression patterns were examined by applying the cell extracts of fibroblast treated with the increasing concentrations of tocotrienol on two-dimensional gel electrophoresis(2-D gel electrophoresis). As the concentrations increasing, many proteins began to appear with the increasing amounts, while several proteins diminished or disappeared. From these results, tocotrienol was clearly shown to have abilities on protecting any oxidizing damages and stimulating anti-oxidizing activities of the organisms.

• BMB Reports
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• v.39 no.2
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• pp.216-222
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• 2006

In the present study, we compared six different solubilization buffers and optimized two-dimensional electrophoresis (2-DE) conditions for human lymph node proteins. In addition, we developed a simple protocol for 2-D gel storage. Efficient solubilization was obtained with lysis buffers containing (a) 8M urea, 4% CHAPS (3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate), 40 mM Tris base, 65 mM DTT(dithiothreitol) and 0.2% carrier ampholytes; (b) 5M urea, 2M thiourea, 2% CHAPS, 2% SB 3-10 (N-decyl-N, N-dimethyl-3-ammonio-1-propanesulfonate), 40mM Tris base, 65 mM DTT and 0.2% carrier ampholytes or (c) 7M urea, 2M thiourea, 4% CHAPS, 65 mM DTT and 0.2% carrier ampholytes. The optimal protocol for isoelectric focusing (IEF) was accumulated voltage of 16,500 Vh and 0.6% DTT in the rehydration solution. In the experiments conducted for the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), best results were obtained with a doubled concentration (50 mM Tris, 384 mM glycine, 0.2% SDS) of the SDS electrophoresis buffer in the cathodic reservoir as compared to the concentration in the anodic reservoir (25 mM Tris, 192 mM glycine, 0.1% SDS). Among the five protocols tested for gel storing, success was attained when the gels were stored in plastic bags with 50% glycerol. This is the first report describing the successful solubilization and 2D-electrophoresis of proteins from human lymph node tissue and a 2-D gel storage protocol for easy gel handling before mass spectrometry (MS) analysis.