• Asian-Australasian Journal of Animal Sciences
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• v.24 no.5
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• pp.685-695
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• 2011

Satellite cells are skeletal muscle progenitor/stem cells that reside between the basal lamina and plasma membranes of skeletal fibers in vivo. These cells can give rise to both myogenic and adipogenic cells. Given the possible role for differentiation of satellite cells into adipocytes in marbling and in some pathological disorders like sarcopenia, knowledge of the proteins involved in such process remains obscure. Using two-dimensional polyacrylamide gel electrophoresis coupled with mass spectrometry, we investigated the proteins that are differentially expressed during adipogenic differentiation of satellite cells from bovine longissimus muscle. Our proteome mapping strategy to identify the differentially expressed intracellular proteins during adipogenic differentiation revealed a total of 25 different proteins. The proteins up-regulated during adipogenic differentiation of satellite cells like Cathepsin H precursor, Retinal dehydrogenase 1, Enoyl-CoA hydratase, Ubiquinol-cytochrome-c reductase, T-complex protein 1 subunit beta and ATP synthase D chain were found to be associated with lipid metabolism. The down-regulated proteins like LIM protein, annexin proteins, cofilin-1, Rho GDP-dissociation inhibitor 1 and septin-2, identified in the present study were found to be associated with myogenesis. These results clearly demonstrate that the adipogenic conversion of muscle satellite cells is associated with the up-regulated and down-regulated proteins involved in adipogenesis and myogenesis respectively.

• BMB Reports
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• v.42 no.7
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• pp.433-438
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• 2009

The objective of this study was to identify proteins in the m. longissimus dorsi between early (12 months of age) and late (27 months of age) fattening stages of Hanwoo (Korean cattle) steers. Using two-dimensional electrophoresis and mass spectrometry, 8 proteins of 11 differentially expressed spots between the 12 and 27 month age groups were identified in the loin muscle. Among those that were differentially expressed, zinc finger 323 and myosin light chain were highly expressed in late-fattening stage, and two catabolic enzymes, triosephosphate isomerase (TPI) and succinate dehydrogenase (SDH) were expressed more in the early versus the late-fattening stage. In particular, the quantification of TPI and SDH by immunoblotting correlated well with fat content. Our data suggested that TPI and SDH are potential candidates as markers and their identification provides new insight into the molecular mechanisms and pathways associated with intramuscular fat contents of bovine skeletal muscle.

• Journal of Microbiology and Biotechnology
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• v.17 no.6
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• pp.934-944
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• 2007

Paenibacillus polymyxa E681 is known to be able to suppress plant diseases by producing antimicrobial compounds and to promote plant growth by producing phytohormones, and secreting diverse degrading enzymes. In spite of these capabilities, little is known regarding the flow of information from the bacterial strain to the barley roots. In an attempt to determine the flow of information from the bacterial strain to barley roots, the strain was grown in the presence and absence of barley, and two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and MALDI-TOF mass spectrometry were used. 2D-PAGE detected approximately 1,000 spots in the cell and 1,100 spots in the supernatant at a pH 4-10 gradient. Interestingly, about 80 spots from each sample showed quantitative variations. Fifty-three spots from these were analyzed by MALDI-TOF mass spectrometry and 28 proteins were identified. Most of the cytosolic proteins expressed at higher levels were found in P. polymyxa E681 cells grown in the presence of barley rather than in the absence of barley. Proteins detected at a lower level in the surpernatant of P. polymyxa E68l cells grown in the presence of barley were lipoprotein, glucose-6-phosphate 1-dehydrogenase, heat-shock protein HtpG, spermidine synthase, OrfZ, ribonuclease PH, and coenzyme PQQ synthesis protein, and flagellar hook-associated protein 2 whereas proteins detected at a higher level in the surpernatant of P. polymyxa E681 cells grown in the presence of barley included D-alanyl-D-alanine ligase A, isopentenyl-diphosphate delta-isomerase, ABC transporter ATP-binding protein Uup, lipase. Many of the proteins belonging to plant-induced stimulons are associated with biosynthetic metabolism and metabolites of proteins and transport. Some of these proteins would be expected to be induced by environmental changes resulting from the accumulation of plant-secreted substances.

• Journal of Marine Bioscience and Biotechnology
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• v.2 no.1
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• pp.68-72
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• 2007

Flounder is one of the major aquacultured fish and of an economically important item in Korean fisheries. Recently, there are trends of research worldwide that aim to analyze and characterize a whole genome or a whole proteome of interesting species. The data are utilized for the understanding and development of preventive and curative technologies for the serious diseases. However, there are very limited information of proteome for marine organisms, we optimized first the conditions for two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) with serum form a marine fish, flounder (Paralichthys olivaceus). A pre-treatment of serum and an optimization of protein concentration analyzed were surveyed for enhancing the separation for proteins. A statistical analysis was performed on the overall 1,820 protein spots to overcome the variability among individual fishes.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.131-131
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• 2017

Though the Platycodon grandiflorum, has a broad range of pharmacologic properties, but the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two-dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}2-fold$) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, the frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). Taken together, the protein profile may provide insight clues for better understanding the characteristics of proteins and its metabolic activities in various explants of this essential medicinal plant P. grandiflorum.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.132-132
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• 2017

Plants, including Platycodon grandiflorum have been used globally across varied cultures as a safe natural source of medicines. From time immemorial, humans have relied on plants that could meet their basic necessities such as food, shelter, fuel and health. This study was executed to profile proteins from the hormone induced diploid and tetraploid roots using high throughput proteome approach. Two dimensional gels stained with CBB, a total of 64 differential expressed proteins were identified from the diploid root using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 20 differential expressed protein spots ( ${\geq}1.5-fold$) were analyzed using LTQ-FTICR MS whereas a total of 13 protein spots were up regulated and 7 protein spots were down-regulated. However, in the case of tetraploid root, a total of 78 differential expressed proteins were identified from tetraploid root of which a total of 28 differential expressed protein spots (${\geq}1.5-fold$) were analyzed by mass spectrometry whereas a total of 16 protein spots were up regulated and a total of 12 protein spots were down-regulated. However, proteins identified using iProClass databases revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding, oxidoreductase activity, transporter activity and isomers activity. The exclusive protein profile may provide insight clues for better understanding the characteristics of protein function and its metabolic activity that can help for the development of the nutritional and breeding aspects of this economically important medicinal plant.

• Current Research on Agriculture and Life Sciences
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• v.31 no.1
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• pp.30-37
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• 2013

Bacillus subtilis and Bacillus amyloliquefaciens are closely related species that share a similar genomic background, and are both known to secrete large amounts of proteins directly into a medium. The extracellular proteomes of two strains of Bacillus subtilis and two strains of Bacillus amyloliquefaciens were compared by 2-D gel electrophoresis during the late exponential growth phase. The relative abundance of some minor protein spots varied among the four strains of Bacillus. Over 123 spots of extracellular proteins were visualized on the gel for B. subtilis CH 97, 68 spots for B. subtilis 3-5, 230 spots for B. amyloliquefaciens CH 51, and 60 spotsfor B. amyloliquefaciens 86-1. 2D gel electrophoresis images of the four Bacillus strains showed significantly different protein profiles. Consistent with the 2D gel electrophoretic analysis, most of the B. subtilis proteins differed from the proteases secreted by the B. amyloliquefaciensstrains. Among the proteins identified from B. subtilis, approximately 50% were cytoplasmic and 30% were canonically extracellular proteins. The secreted protein profiles for B. subtilis CH 97 and B. subtilis 3-5 were quite different, as were the profiles for B. amyloliquefaciens CH 51 and 86-1. The four proteomes also differed in the major protein composition. The B. subtilis CH 97 and B. amyloliquefaciens CH 51 proteomes both contained large amounts of secreted hydrolytic enzymes. Among the four strains, B. subtilis 3-5 secreted the least number of proteins. Therefore, even closely related bacteria in terms of genomic sequences can still have significant differences in their physiology and proteome layout.

• Journal of the Korea Society for Simulation
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• v.20 no.2
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• pp.77-85
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• 2011

It is believed that the anomalies or diseases of human organs are identified by the analysis of the patterns. This paper proposes a new classification technique for the identification of cancer disease using the proteome patterns obtained from two-dimensional polyacrylamide gel electrophoresis(2-D PAGE). In the new classification method, three different classification methods such as support vector machine(SVM), multi-layer perceptron(MLP) and k-nearest neighbor(k-NN) are extended by multi-boosting method in an array of subclassifiers and the results of each subclassifier are merged by ensemble method. Genetic algorithm was applied to obtain optimal feature set in each subclassifier. We applied our method to empirical data set from cancer research and the method showed the better accuracy and more stable performance than single classifier.

• Genomics & Informatics
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• v.7 no.4
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• pp.203-207
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• 2009

The target of rapamycin (TOR) signaling pathway conserved from yeast to human plays critical roles in regulation of eukaryotic cell growth. It has been shown that TOR pathway is involved in several cellular processes, including ribosome biogenesis, nutrient response, autophagy and aging. However, due to the functional diversity of TOR pathway, we do not know yet some key effectors of the pathway. To find unknown effectors of TOR signaling pathway, we took advantage of a green fluorescent protein (GFP)-tagged collection of budding yeast Saccharomyces cerevisiae. We analyzed protein abundance changes by measuring the GFP fluorescence intensity of 4156 GFP-tagged yeast strains under inhibition of TOR pathway. Our proteomic analysis argues that 83 proteins are decreased whereas 32 proteins are increased by treatment of rapamycin, a specific inhibitor of TOR complex 1 (TORC1). We found that, among the 115 proteins that show significant changes in protein abundance under rapamycin treatment, 37 proteins also show expression changes in the mRNA levels by more than 2-fold under the same condition. We suggest that the 115 proteins indentified in this study may be directly or indirectly involved in TOR signaling and can serve as candidates for further investigation of the effectors of TOR pathway.

• Biomedical Science Letters
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• v.23 no.4
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• pp.395-401
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• 2017

Various preclinical and clinical trials have been conducted the efficacy of celastrol. In data presented in the current manuscript is the first trial to inhibit Helicobacter pylori with celastrol. In this study, the quantitative change of various H. pylori proteins including CagA and VacA by the anti-bacterial effect of celastrol was determined. The anti-H. pylori effects of celastrol was investigated by performing 2-dimensional electrophoresis and additional supporting experiments. After 2-dimensional electrophoresis analysis, spot intensities were analyzed and then each spot was identified using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) or peptide sequencing using Finnigan LCQ ion trap mass spectrometer (LC-MS/MS). The results show that celastrol has multiple effects on protein expression in H. pylori.