• YAKHAK HOEJI
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• v.54 no.3
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• pp.180-186
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• 2010

Aldosterone, mineralocorticoid hormone, has important functions related to the regulation of blood pressure and balance of fluids and electrolytes in the distal region of the nephron. By genomic and non-genomic action of aldosterone, the physiological kidney functions are modulated. However, many of them except several kind of sodium channel have not been identified and analyzed yet. In this study, proteomic technologies with two-dimensional gel electrophoresis (2-DE) gel using aldosterone rat model were applied to analyze and identify the aldosterone dependently expressed proteins in rat kidney cortex. As a result, the established aldosterone rat model exhibited the normal physiological responses to aldosterone and modulated proteins were identified, which included 15 increased and 3 decreased proteins on 2-DE analysis. Among them, 11 proteins were identified as changed proteins by LC-MS/MS analysis. These proteins identified as aldosterone induced proteins were involved in several cellular pathways such as cytoskeleton remodeling, energy metabolism, amino acid metabolism, and chaperone process. In conclusion, our data could provide the insights into the new mechanism underlying regulation of kidney functions by aldosterone.

• The KIPS Transactions:PartD
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• v.15D no.5
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• pp.681-690
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• 2008

In proteomics research, the identification of differentially expressed proteins observed under specific conditions is one of key issues. There are several ways to detect the change of a specific protein's expression level such as statistical analysis and graphical visualization. However, it is quiet difficult to handle the spot information of an individual protein manually by these methods, because there are a considerable number of proteins in a tissue sample. In this paper, using database and data mining techniques, the application plan of OLAP data cube and Discovery-driven exploration is proposed. By using data cubes, it is possible to analyze the relationship between proteins and relevant clinical information as well as analyzing the differentially expressed proteins by disease. We propose the measure and exception indicators which are suitable to analyzing protein expression level changes are proposed. In addition, we proposed the reducing method of calculating InExp in Discovery-driven exploration. We also evaluate the utility and effectiveness of the data cube and Discovery-driven exploration in the lung cancer 2-DE gel image.

• Journal of Aquaculture
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• v.10 no.3
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• pp.301-310
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• 1997

To investigate a possibility of the species genetic relationship for the soluble proteins analysis on the class Cephalopoda in the Yellow Sea, the isolate eye, muscle and liver proteins from five species (Sepia esculenta, Sepiella japonica, Loligo chinensis, Loligo beka and Octopus minor) were analysed using different electrophoretic techniques (Davis-polyacrylamide gel electrophoresis, SDS-PAGE, exponential gradient SDS-PAGE, thin-layer isoelectro-focusing and two-dimensional PAGE). The average molecular weight of the soluble eye and muscle proteins was estimated at 35-50 KDa, separated b the exponential gradient SDS-PAGE. It was corresponds to that of electrophoretic patterns by t재 dimensional PAGE. By which the thin layer IEF, the target proteins showed a reasonable specificity based on their isoelectric points (pI) 7.5-8.5.

• Toxicological Research
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• v.20 no.2
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• pp.89-100
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• 2004

The comet assay (also called the single-cell gel electrophoresis assay) has been widely used for detecting DNA damage and repair in individual cells. Since the conventional methods of evaluating comet assay data using frequency statistics are unsatisfactory we developed a new quantitative measure of DNA damage/repair that is based on all information residing in the dose/time-response curves of a comet experiment. Blood samples were taken from 25 breast cancer patients before undergoing radiotherapy. The comet assay was performed under alkaline conditions using isolated lymphocytes. Tail DNA, tail length, tail moment and tail inertia of the comet were measured for each patient at four doses of $\gamma$-rays (0, 2, 4 and 8 Gy) and at four time points after irradiation (0, 10, 20 and 30 min) using 100 cells each. The resulting three-dimensional dose-time response surface was modeled by multiple regression, and the second derivative, termed 2D, on dose and time was determined. A software module was programmed in SAS/AF to compute 2D values. We applied the new method successfully to data obtained from cancer patients to be assessed for their radiation sensitivity. We computed the 2D values for the four damage measures, i.e., tail moment, tail length, tail DNA and tail inertia, and examined the pairwise correlation coefficients of 2D both on the log scale and the unlogged scale. 2D values based on tail moment and tail DNA showed a high correlation and, therefore, these two damage measures can be used interchangeably as far as DNA repair is concerned. 2D values based on tail inertia have a correlation profile different from the other 2D values which may reflect different facets of DNA damage/repair. Using the dose-time response surface, other statistical models, e.g., the proportional hazards model, become applicable for data analysis. The 2D approach can be applied to all DNA repair measures, Le., tail moment, tail length, tail DNA and tail inertia, and appears to be superior to conventional evaluation methods as it integrates all data of the dose/time-response curves of a comet assay.

• Molecules and Cells
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• v.40 no.9
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• pp.685-695
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• 2017

Obesity and the metabolic disorders that constitute metabolic syndrome are a primary cause of morbidity and mortality in the world. Nonetheless, the changes in the proteins and the underlying molecular pathways involved in the relevant pathogenesis are poorly understood. In this study a proteomic analysis of the visceral adipose tissue isolated from metabolically healthy and unhealthy obese patients was used to identify presence of altered pathway(s) leading to metabolic dysfunction. Samples were obtained from 18 obese patients undergoing bariatric surgery and were subdivided into two groups based on the presence or absence of comorbidities as defined by the International Diabetes Federation. Two dimensional difference in-gel electrophoresis coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was carried out. A total of 28 proteins were identified with a statistically significant difference in abundance and a 1.5-fold change (ANOVA, $p{\leq}0.05$) between the groups. 11 proteins showed increased abundance while 17 proteins were decreased in the metabolically unhealthy obese compared to the healthy obese. The differentially expressed proteins belonged broadly to three functional categories: (i) protein and lipid metabolism (ii) cytoskeleton and (iii) regulation of other metabolic processes. Network analysis by Ingenuity pathway analysis identified the $NF{\kappa}B$, IRK/MAPK and PKC as the nodes with the highest connections within the connectivity map. The top network pathway identified in our protein data set related to cellular movement, hematological system development and function, and immune cell trafficking. The VAT proteome between the two groups differed substantially between the groups which could potentially be the reason for metabolic dysfunction.

• Journal of Radiation Industry
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• v.6 no.2
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• pp.129-138
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• 2012

Proteomic analysis was performed in order to identify proteomic changes by salt stress between the Japonica cv. Donganbyeo (WT) and two salt-tolerant (ST) mutant lines by using the SDS-PAGE and 2-DE. Two salt tolerant rice mutant lines, ST-87 and ST-301, were selected by in vitro mutagenesis with gamma-ray. Three-week-old seedlings were treated with 171 mM NaCl for 7 days. In the SDS-PAGE, three proteins with molecular weights of 27, 46 and 58 kDa were highly increased under salt treatment. Total proteins from shoots of both WT and ST-lines were separated by two-dimensional gel electrophoresis. In 2-DE, 201, 226, 217 and 213 protein spots were detected in the untreated-or treated-WT and untreated- or treated-ST-87, respectively. Of theses, 17 and 10 protein spots were up- and down-regulated under salt stress in the WT, respectively. While, 16 and 8 protein spots were up- and down-regulated under salt stress in the ST-87, respectively, compared with the untreated plants. High intensity or de novo synthesized proteins were analyzed by MALDI-TOF/MS analysis.

• Journal of Plant Biology
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• v.34 no.2
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• pp.121-127
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• 1991

Total soluble proteins from three developmental stages of induced root nodules of Canavalia lineata were compared with those of non-nodulated roots by SDS-PAGE and two dimensional (2-D) gel electrophoresis. Thirteen nodule-specific protein (nodulin) bands were identified by the former and 30 nodule specific protein spots were detected by the latter method respectively. Some of the nodulins were detected differentially depending on the nodule's developmental stages. For example, only three leghemoglobin (Lb)-like protein spots appeared at stage I (d<2 mm), but two additional Lb-like protein spots appeared at stage II (d <4-5 mm). pI value and molecular weight of nomomers of Lb-like protein were narrower and greater than those of soybean, ranging from 4.4 to 5.0 and 15.7 kd respectively. Northern blot hybridization of total RNAs from roots and root nodules using soybean Lb cDNA as a probe made it clear that Lb gene was expressed tissue-specifically only in the root nodules.odules.

• Korean Journal of Food Science and Technology
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• v.43 no.1
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• pp.12-16
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• 2011

This study was conducted to identify the differences in proteomic characteristics between Ca-enriched king oyster mushrooms and general king oyster mushrooms. A combined high-throughput proteomic approach was employed to determine the expression profiles and identity of proteins using 2-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. The overall distribution patterns of the proteins were quite similar, but many of the protein spot intensities varied. A total of 10 proteins, representing a significant difference in the quantities of protein betweenthe two types of mushrooms, were successfully identified. Among these proteins, eight kinds were increased in the Ca-enriched king oyster mushrooms and two kinds were decreased. This study showed that proteomic analysis can help define specific changes in protein level and composition, which can occur in mushrooms where Ca content may or may not be enriched.

• Korean Journal of Veterinary Research
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• v.50 no.4
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• pp.285-295
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• 2010

Protein expression patterns in Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) strains with diverse phenotypes, such as phage type, antibiotic resistance pattern and plasmid profiles were examined. For detailed analysis of proteins expressed by different S. Typhimurium strains, protein fractions were divided into detergent-rich phase (DP) and aqueous phase (AP) using triton X-114 detergent. The two phases were subjected to two-dimensional gel electrophoresis (2-DE), followed by protein identification using peptide mass fingerprinting (PMF). In the results, PMF showed that DP fractions consisted mainly of outer membrane proteins, whereas the AP fractions included cytosolic proteins. Comparison of 2-DE profiles of DP did not show any distinct protein spots which could be correlated with phage type, antibiotic resistance pattern or plasmid profile. However, comparisons of 2-DE profiles of the AP revealed differences in the protein spots, which could be correlated with the plasmid profile and phage types. Among these protein spots, flagellin was specific for strains containing a 90 kb plasmid. Compared to DT193 phage type, three protein spots in the range of pI 5.0-5.5 and MW 8-15 kDa of AP 2-DE profiles were absent in the DT104 phage types. Additionally, a protein spot with PI in the range of 4.5-5.0 and molecular weight (MW) between 51-69 kDa was specific for phage type DT104, while a protein spot with pI in the range of 4.0-4.8 and MW between 18-20 kDa was specific for DT193 phage type. These protein spots may be useful for discriminating phage types of S. Typhimurium.

• The Plant Pathology Journal
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• v.24 no.2
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• pp.191-201
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• 2008

Bacillus sp. SB-007 was isolated from pea leaves harvested from the southwestern parts of South Korea through screening on a minimal medium containing 0.2% purified cutin for its ability to induce the cutinase production. However, no cutinase was produced when it was grown in a minimal medium containing 0.2% glucose. A proteomic approach was applied to separate and characterize these differentially secreted proteins. The expression level of 83 extracellular proteins of the cutinase-producing Bacillus sp. strain SB-007 incubated in a cutinase-induced medium increased significantly as compared with that cultured in a non cutinase-induced medium containing glucose. The extracellular proteome of Bacillus sp. SB-007 includes proteins from different functional classes, such as enzymes for the degradation of various macromolecules, proteins involved in energy metabolism, sporulation, transport/binding proteins and lipoproteins, stress inducible proteins, several cellular molecule biosynthetic pathways and catabolism, and some proteins with an as yet unknown function. In addition, the two protein spots showed little similarities with the known lipolytic enzymes in the database. These secreted proteome analysis results are expected to be useful in improving the Bacillus strains for the production of industrial cutinases.