• Journal of Applied Biological Chemistry
• /
• v.51 no.3
• /
• pp.88-94
• /
• 2008

Three different protein extraction methods-phenol extraction, trichloroacetic acid (TCA) precipitation, and desalting/TCA precipitation-were compared to determine the optimal reproducible high resolution 2-dimensional (2-D) electrophoresis for each chungkugjang, doenjang, and kochujang samples. The soluble proteins from Chungkugjang extracted by phenol were separated with high reproducibility and resolution, and gained 1.75- to 3-fold more protein spots on 2-D gel than those from the other methods. On the contrary, the extracted proteins from doenjang and kochujang treated by desalting/TCA precipitation method showed about 1.5- to 3.3-fold more protein spots on 2-D gel. Using the established methods, the changes in the protein profiles of the fermented soy foods were monitored during the fermentation period by 2-DE. One of the major proteins in soy, $\beta$-conglycinin $\alpha$-subuint, and some proteins with unknown functions were localized on 2-D gel as the protease-resistant proteins throughout the fermentation period of doenjang. Changes in the protein profile monitored by the established methods can provide basic information on unfolding the mechanisms of the generation of biofunctional activity in the fermented soy foods.

• Preventive Nutrition and Food Science
• /
• v.13 no.4
• /
• pp.366-369
• /
• 2008

Proteins secreted from bifidobacteria are believed to play important roles in human intestines via interacting with different host cells. In this respect, proteins secreted from Bifidobacterium pseudocatanulatum BP1, which has been rarely studied, were analyzed by two-dimensional gel electrophoresis (2DE). Using this approach, approx-imately 21 protein spots on a 2DE gel were detected and 10 of these spots were identified by mass spectrometry. Five spots were identified as hypothetical proteins and the remaining 5 spots were identified as a putative iron-side-rophore binding lipoprotein, a short-chain dehydrogenase/reductase SDR, an exonuclease, cytochrome P450 hydroxylase, and a putative dehydrogenase. The identification of secreted putative iron-siderophore binding lipoprotein was highly interesting since it is an important protein that is involved in ferric iron uptake in pathogenic bacteria. This finding could accelerate studies on the probiotic effect of Bifidobacterium by explaining the competition between bifidobacteria and intestinal pathogens for ferric iron.

• BMB Reports
• /
• v.37 no.3
• /
• pp.298-303
• /
• 2004

In general, a SYPRO Ruby dye is well known as a sensitive fluorescence-based method for detecting proteins by one-or two-dimensional SDS-PAGE (1-DE or 2-DE). Based on the SYPRO Ruby dye system, the combined two-dimensional fibrin zymography (2-D FZ) with SYPRO Ruby staining was newly developed to identify the Bacillus sp. proteases. Namely, complex protein mixtures from Bacillus sp. DJ-4, which were screened from Doen-Jang (Korean traditional fermented food), showed activity on the zymogram gel. The gel spots on the SYPRO Ruby gel, which corresponded to the active spots showing on the 2-D FZ gel, were analyzed by a matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometric analysis. Five intracellular fibrinolytic enzymes of Bacillus sp. DJ-4 were detected through 2-D FZ. The gel spots on the SYPRO Ruby dye stained 2-D gel corresponding to 2-D FZ were then analyzed by MALID TOF MS. Three of the five gel spots proved to be quite similar to the ATP-dependent protease, extracellular neutral metalloprotease, and protease of Bacillus subtilis. Also, the extracellular proteases of Bacillus sp. DJ-4 employing this combined system were identified on three gels (e.g., casein, fibrin, and gelatin) and the proteolytic maps were established. This combined system of 2-D zymography and SYPRO Ruby dye should be useful for searching the specific protease from complex protein mixtures of many other sources (e.g., yeast and cancer cell lines).

• BMB Reports
• /
• v.32 no.5
• /
• pp.445-450
• /
• 1999

We purified and characterized a bovine pregnancy-associated protein in pregnant cow urine using two-dimensional gel electrophoresis. Urine from cows was collected according to their status of pregnancy and non-pregnancy. Proteins in the cow urine were fractionated with 50% ammonium sulfate prior to two-dimensional gel electrophoresis. Proteins separated on the gels were compared in terms of expression level and new expression by molecular mass and isoelectric point. We localized two pregnancy-associated protein spots on the gels at molecular masses of 24 kDa and 20 kDa and isoelectric points of 5.5 and 5.7, respectively. Likewise, two non-pregnancy specific proteins were localized at 27 kDa and 28 kDa with isoelectric points of 5.7 and 5.9, respectively. To rule out the possibility that environmental or genetic factors might influence the expression of the proteins, we demonstrated the pregnancy-associated expression of the proteins in two-dimensional gels with pregnant urine taken from cows raised in a different institute. The pregnancy-associated protein with molecular mass of 20 kDa and isoelectric point of 5.7, namely spot 2, was microsequenced and found to be highly homologous to the bovine collagen alpha 1 chain.

• Bulletin of the Korean Chemical Society
• /
• v.23 no.11
• /
• pp.1511-1512
• /
• 2002

• Journal of Microbiology and Biotechnology
• /
• v.17 no.1
• /
• pp.89-95
• /
• 2007

Improvements in the dissolution of proteins in two-dimensional gel electrophoresis have greatly advanced the ability to analyze the proteomes of microorganisms under a wide variety of physiological conditions. This study examined the effect of various combinations of chaotropic agents, a reducing agent, and a detergent on the dissolution of the Streptomyces peucetius cytosolic proteins. The use of urea alone in a rehydration buffer as a chaotropic agent gave the proteome a higher solubility than any of the urea and thiourea combinations, and produced the highest resolution and clearest background in two-dimensional gel electrophoresis. Two % CHAPS, as a detergent in a rehydration buffer, improved the protein solubility. After examining the effect of several concentrations of reducing agent, 50 mM DTT in a rehydration buffer was found to be an optimal condition for the proteome analysis of Streptomyces. Using this optimized buffer condition, more than 2,000 distinct and differentially expressed soluble proteins could be resolved using two-dimensional gel electrophoresis with a pI ranging from 4-7. Under this optimized condition, 15 novel small proteins with low-level expression, which could not be analyzed under the non-optimized conditions, were identified. Overall, the optimized condition helped produce a better reference gel for Streptomyces peucetius.

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

• Preventive Nutrition and Food Science
• /
• v.2 no.4
• /
• pp.281-284
• /
• 1997

Heat-induced gelation is an important functional property of whey proteins. Preheating of calcium reduced whey was reported to increase gel strength. 5% whey-protein solutions were preheated at pH7 and at various temperatures(60~8$0^{\circ}C$) for 15 minutes. The amount of soluble aggregates and denaturation enthalpy of preheated whey proteins were measured. Preheating temperature was negatively correlated with denaturation enthalpy($R^2$=0.857, P=0.08) and positive with the amount of soluble aggregates($R^2$=0.921, P=0.002). Denaturation enthalpy was negatively correlated with gel strength($R^2$=0.93, P=0.002). Soluble aggregates and gel strength were positively correlated($R^2$=0.972, P=0.0003). The formation of three dimensional gel network requires controlled protein denaturation and aggregation. Since preheating leads to the partial denaturation of proteins and the formation of soluble aggregates, preheated whey proteins have a higher gel strength than non-preheated one.

• Journal of the Korean Mathematical Society
• /
• v.33 no.4
• /
• pp.993-1008
• /
• 1996

The white noise analysis, initiated by Hida [3] in 1975, has been developed to an infinite dimensional distribution theory on Gaussian space $(E^*, \mu)$ as an infinite dimensional analogue of Schwartz distribution theory on Euclidean space with Legesgue measure. The mathematical framework of white noise analysis is the Gel'fand triple $(E) \subset (L^2) \subset (E)^*$ over $(E^*, \mu)$ where $\mu$ is the standard Gaussian measure associated with a Gel'fand triple $E \subset H \subset E^*$.

• Nuclear Engineering and Technology
• /
• v.49 no.1
• /
• pp.189-195
• /
• 2017

Gel dosimeters have unique advantages in comparison with other dosimeters. Until now, these gels have been used in different radiotherapy techniques as a reliable dosimetric tool. Because dose distribution measurement is an important factor for appropriate treatment planning in different radiotherapy techniques, in this study, we evaluated the ability of the N-isopropylacrylamide (NIPAM) polymer gel to record the dose distribution resulting from the mixed neutron-gamma field of boron neutron capture therapy (BNCT). In this regard, a head phantom containing NIPAM gel was irradiated using the Tehran Research Reactor BNCT beam line, and then by a magnetic resonance scanner. Eventually, the $R_2$ maps were obtained in different slices of the phantom by analyzing T2-weighted images. The results show that NIPAM gel has a suitable potential for recording three-dimensional dose distribution in mixed neutron-gamma field dosimetry.