• Journal of Biomedical Engineering Research
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• v.28 no.5
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• pp.601-608
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• 2007

2 Dimensional Gel Electrophoresis(2DGE) is an essentialmethodology for analysis on the expression of various proteins. For example, information for the location, mass, expression, size and shape of the proteins obtained by 2DGE can be used for diagnosis, prognosis and biological progress by comparison of patients with the normal persons. Protein spot matching for this purpose is comparative analysis of protein expression pattern for the 2DGE images generated under different conditions. However, visual analysis of protein spots which are more than several hundreds included in a 2DGE image requires long time and heavy effort. Furthermore, geometrical distortion makes the spot matching for the same protein harder. In this paper, an iterative algorithm is introduced for more efficient spot matching. Proposed method is first performing global matching step, which reduces the geometrical difference between the landmarks and the spot to be matched. Thus, movement for a spot is defined by a weighted sum of the movement of the landmark spots. Weight for the summation is defined by the inverse of the distance from the spots to the landmarks. This movement is iteratively performed until the total sum of the difference between the corresponding landmarks is larger than a pre-selected value. Due to local distortion generally occurred in 2DGE images, there are many regions in whichmany spot pairs are miss-matched. In the second stage, the same spot matching algorithm is applied to such local regions with the additional landmarks for those regions. In other words, the same method is applied with the expanded landmark set to which additional landmarks are added. Our proposed algorithm for spot matching empirically proved reliable analysis of protein separation image by producing higher accuracy.

• YAKHAK HOEJI
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• v.50 no.4
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• pp.268-271
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• 2006

Protein kinase UL97 is an unusual protein kinase that can phosphorylate nucleoside analogs as well as protein/peptide. Previously we found a H2B-derived peptide, KESYSVYVYKV and reported that the P+5 position (K) is important. To further understand the substrate specificity at the P+5 position, we introduced spot assay system and showed that a peptide containing K residue among other amino acids at the P+5 position is the best substrate. Also other residues such as M, I, L, or G are good enough to be substrate of UL97. This result may aid the discovery of a new antiviral inhibitor.

• 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.

• International Journal of Industrial Entomology and Biomaterials
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• v.9 no.1
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• pp.117-121
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• 2004

The patterns of diapause-associated proteins of silkworm eggs were analyzed by two-dimensional (2-D) gel electrophoresis. Among the hundreds of spots on the 2-D gels, at least two proteins were considered to be associated with diapause. A protein, spot 4, with an approximate molecular weight of 38 kDa and pI 6.1 was observed in the HCI-treated, cold-treated, and diapause eggs, respectively. Spot 4 was undetectable in unfertilized eggs and non-diapause eggs at two days after oviposition, suggesting that this protein may be associated with the entrance to diapause. A protein, spot 11, with an approximate molecular weight of 21 kDa and pI of 61 was detected in the unfertilized, HCl-treated, and cold-treated eggs, respectively, after oviposition by normal moths. In diapausing eggs, a protein corresponding to spot 11 was observed in 3-, 5-, and 30-day-old eggs, while the protein was not detected one-day-old eggs. The protein corresponding to spot 11 was not detected in unfertilized and non-diapause eggs obtained from subesophabeal ganglion (SG)-extirpated moths either. Spot 11 was also considered to be a diapause specific protein, which occurred at only early embryonic stage under the control of diapause-downregulated gene.

• BMB Reports
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• v.37 no.6
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• pp.726-734
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• 2004

White spot disease (WSD) is caused by the white spot syndrome virus (WSSV), which results in devastating losses to the shrimp farming industry around the world. However, the mechanism of virus entry and spread into the shrimp cells is unknown. A binding assay in vitro demonstrated VP28-EGFP (envelope protein VP28 fused with enhanced green fluorescence protein) binding to shrimp cells. This provides direct evidence that VP28-EGFP can bind to shrimp cells at pH 6.0 within 0.5 h. However, the protein was observed to enter the cytoplasm 3 h post-adsorption. Meanwhile, the plaque inhibition test showed that the polyclonal antibody against VP28 (a major envelope protein of WSSV) could neutralize the WSSV and block an infection with the virus. The result of competition ELISA further confirmed that the envelope protein VP28 could compete with WSSV to bind to shrimp cells. Overall, VP28 of the WSSV can bind to shrimp cells as an attachment protein, and can help the virus enter the cytoplasm.

• Childhood Kidney Diseases
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• v.4 no.1
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• pp.1-5
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• 2000

Purpose: The plcr of spot urine has been uised to predict the timed urine protein excretion. Although this method reduces errors caused by variations in urine volume, it is relatively thconvenient and expensive. Recently, a more rapid and less expensive screening method with specific gravity(SG) has been reported, and we have examined whether estimated-creatinine(Cr-est) with urine 5G could be used in place of urine creatinine to predict 24-hour collected urine protein excretion in children. Methods: We had retrospectively analyzed protein, creatinine and urine SG in randomized spot urine samples of 147 patients from March 1998 till June 1998 in Korea university Guro hospital and compared the urinary protein creatinine ratio(P/Cr) with the protein estimated-creatinine ratio(P/Cr-est). We compared the correlation of urinary creatinine vs-urine 5G with the timed urine pretein excretion. Results: 1) urine SG accurately estimated urine creatinine concentration (r=0.407, P<0.001, Cr=SG x 4485.82-4482.87). 2) P/Cr correlated with urine protein excretion measured in a 24-hour urine collection (r=0.771, P<0.001, 24-hour collected urine protein : 0.338 x (P/Cr) 4+667.885). 3) P/Cr-est correlated with a 24-hour collected urine protein (r=0.723, P<0.001, 24-hour collected urine protein =0.354 x (P/Cr-est)+726.044), Conclusions: These results suggest that P/Cr-est with urine SG could be useful method for screening proteinuria in children.

• Journal of Veterinary Clinics
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• v.36 no.1
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• pp.85-87
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• 2019

Eight-week-old Spot-billed duck were presented with visible drooping of both of wings. On physical examination, the Spot-billed ducks revealed valgus deformity of the carpal joint resulting in the primary flight feathers protruding dorsally. The bird was in good body condition and there was no loss of motion in any of the joints in the wings. The bird was fed chicken pellet with 18.5% of protein level and reared in a cage. Based on the clinical presentation and physical examination 'angel wing' was diagnosed. Wing bandage and nutritional change to lower-protein diet with fresh vegetables were applied simultaneously. And duck was transferred to wider outside pen with small pond. Four-week afterward clinical signs of angel wing were improved.

• Korean Journal of Medicinal Crop Science
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• v.22 no.5
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• pp.398-404
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• 2014

Salt stress is one of the major abiotic stresses affecting the yield of ginseng (Panax ginseng C. A. Meyer). The objective of this study was to identify bio-marker, which is early responsive in salt stress in ginseng, using proteomics approach. Ginseng plants were exposed to 5 ds/m salt concentration and samples were harvested at 0, 6, 12 and 18 hours after exposure. Total proteins were extracted from ginseng leaves treated with salt stress using Mg/NP-40 buffer and were separated on high resolution 2-DE. Approximately $1003{\pm}240$ (0 h), $992{\pm}166$ (6 h), $1051{\pm}51$ (12 h) and $990{\pm}160$ (18 h) spots were detected in colloidal CBB stained 2D maps. Among these, 8 spots were differentially expressed and were identified by using MALDI-TOF/TOF MS or/and LC-MS/MS. Ethylene response sensor-1 (spot GL 1), nucleotide binding protein (spot GL 2), carbonic anhydrase-1 (spot GL 3), thylakoid lumenal 17.9 kDa protein (spot GL 4) and Chlorophyll a/b binding protein (spot GL 5, GL 6) were up-regulated at the 12 and 18 hour, while RuBisCO activase B (spot GL 7) and DNA helicase (spot GL 8) were down-regulated. Thus, we suggest that these proteins might participate in the early response to salt stress in ginseng leaves.

• Journal of KIISE:Computing Practices and Letters
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• v.16 no.5
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• pp.551-555
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• 2010

In protein 2-DE image analysis, the accuracy of spot-matching operation which identifies the spot of the same protein in each 2-DE gel image is intensively influenced by the errors caused by the various experimental conditions. This paper proposes an efficient method to find more accurate spot-matching patterns based on multiple reference gel images in spot-matching pattern analysis in protein 2-DE image analysis. Additionally, in order to improve the reduce the execution time which is increased exponentially along with the increasing number of gel images, a "partition then extension" framework is used to find spot-matching pattern of long length and of higher accuracy. In the experiments on real 2-DE images of human liver tissue are used to confirm the accuracy and the efficiency of the proposed algorithm.

• 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.