• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.28-32
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• 2007

The protein phosphorylation is one of the important processes in the cell signaling pathway. A variety of protein kinase families are involved in this process, and each kinase family phosphorylates different kinds of substrate proteins. Many methods to predict the kinase-specific phosphoryrated sites or different types of phosphorylated residues (Serine/Threonine or Tyrosin) have been developed. We employed Supprot Vector Machine (SVM) to attempt the prediction of protein kinase specific phosphorylation sites. 10 different kinds of protein kinase families (PKA, PKC, CK2, CDK, CaM-KII, PKB, MAPK, EGFR) were considered in this study. We defined 9 residues around a phosphorylated residue as a deterministic instance from which protein kinases determine whether they act on. The subsets of PSI-BALST profile was converted to the numerical vectors to represent positive or negative instances. When SVM training, We took advantage of multiple SVMs because of the unbalanced training sets. Representative negative instances were drawn multiple times, and generated new traing sets with the same positive instances in the original traing set. When testing, the final decisions were made by the votes of those multiple SVMs. Generally, RBF kernel was used for the SVMs, and several parameters such as gamma and cost factor were tested. Our approach achieved more than 90% specificity throughout the protein kinase families, while the sensitivities recorded 60% on average.

• Applied Biological Chemistry
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• v.29 no.2
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• pp.212-218
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• 1986

Proteins in Korean rapeseeds, as in many other plantseeds, are usually bound to phytate molecules. These phytate-bound proteins are of little value as foodstuffs because of their poor solubility in digestive systems. Therefore it is necessary to remove phytates from proteins in order to convert these proteins io a useful foodstuff. In the work, an efficient procedure for removal of phytates from defatted Korean rapeseed was found. The influence of pH on the solubility of protein and phytate of rapeseed flour showed that the former was the lowest at pH 5.0 and began to increase as pH further raised. Meanwhile, the latter was the highest at pH 6.0, however, it was decreased abruptly at alkaline pH, especially to content of 1.3% at pH 11.5. The solubility cf protein was relatively high in NaCl aqueous solution at $pH\;6.0{\sim}8.0$, and did not male any noticeable difference depending on NaCl concentration. On the other hand, the solubility of phytate was high at pH of below 6.0 showing an abrupt decrease at pH of above 6.0. The solubility of protein in $CaCl_2$ aqueous solution was highest at $pH\;6.0{\sim}8.0$, however, there was no significant change at the whole range of tested pH of the solution. A maximum solubility of phytate was shown at $pH\;3.0{\sim}4.0$. And it was decreased abruptly at a higher pH of the above range and also decreased at a lower pH with higher $CaCl_2$ concentration. The solubility of phytate in $Na_2SO_3$ aqueous solution was highest at $pH\;5.0{\sim}8.0$. As the concentration goes up the maximum value of solubility was found to move to higher pHs. Depending on the concentration of $Na_2SO_3$, the decreasing pattern was changed in an alkaline solution. The solubility of phytate in the solution containing low concentration of $Ca^{2+}$ ion was low in all treatments at pH of above 7.0 and showed the maximum value at low pH as $Ca^{2+}$ ion concentration increases. The solubility of protein at pH 11.5 showed the highest value in $1mM\;Ca^{2+}$ ion solution.

• BMB Reports
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• v.44 no.7
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• pp.462-467
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• 2011

Up-regulation of selected matrix metalloproteinases (MMPs) such as MMP-9 contributes to inflammatory processes during the development of various skin diseases, such as atopic dermatitis. In this study, we examined the effect of a cell-permeable superoxide dismutase (Tat-SOD) on TNF-${\alpha}$-induced MMP-9 expression in human keratinocyte cells (HaCaT). When Tat-SOD was added to the culture medium of HaCaT cells, it rapidly entered the cells in dose- and time-dependent manners. Tat-SOD decreased TNF-${\alpha}$-induced reactive oxygen species (ROS) generation. Tat-SOD also inhibited TNF-${\alpha}$-induced NF-${\kappa}B$ DNA binding activity. Treatment of HaCaT cells with Tat-SOD significantly inhibited TNF-${\alpha}$-induced mRNA and protein expression of MMP-9, as measured by RT-PCR and Western blot analysis. In addition, Tat-SOD suppressed TNF-${\alpha}$-induced gelatinolytic activity of MMP-9. Taken together, our results indicate that Tat-SOD can suppress TNF-${\alpha}$-induced MMP-9 expression via ROS-NF-${\kappa}B$-dependent mechanisms in keratinocytes, and therefore can be used as an immunomodulatory agent against inflammatory skin diseases related to oxidative stress.

• Journal of Aquaculture
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• v.9 no.2
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• pp.159-166
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• 1996

A feeding experiment was conducted using juvenile Korean rockfish (Sebastes schlegeli) to evaluate supplemental vitamin premix in a test diet containing fish meal as protein source for nutritional study. Four vitamin premixes were prepared by adjusting different quantity and combination of vitamins. Each vitamin premix contained (mg/kg diet) : premix-1 : ascorbic acid, 2666 ; a-tocopheryl acetate, 417 ; thiamin, 60 ; riboflavin, 200 ; pyridoxine, 40 ; niacin, 800 ; Ca-D-pantothenate, 280 ; myo-inositol, 4000 ; D-biotin, 6 ; folic acid, 15 ; p-amino-benjoic acid, 400 ; mennadione, 40 ; A, 16 ; $D_3$, 0.1 ; choline chloride, 8000 ; cyanocobalamin, 0.09 ; premix-2 : ascorbic acid, 270 ; a-tocopheryl acetate, 189 ; thiamin, 13.5 ; riboflavin,, 27 ; pyridoxine, 13.5 ; niacin, 135 ; Ca-D-pantothenate, 135 ; myo-inositol, 135 ; D-biotin, 1. 4 : folic acid, 4.9 ; mennadione, 5.4 : A, 5.4 ; $D_3$, 2.2 ; choline chloride, 3000 ; cyanocobalamin, 0.05 ; premix-3 : ascorbic acid, 570 ; a-tocopheryl acetate, 107 ; thiamin, 20 ; riboflavin, 14.3 ; pyridoxine, 14.3 ; niacin, 71,3 ; Ca-D-pantothenate, 57 ; myo-inositol, 456 ; D-biotin, 0.7 ; folic acid, 2.9 ; p-aminobenjoic acid, 285 ; mennadione, 5.7 ; A, 5.7 ; $D_3$, 1.1 ; choline chloride, 1500 ; cyanocobalamin, 0.03 ; premix-4 : ascorbic acid, 190 : a-tocopheryl acetate, 36 ; thiamin, 6.7 ; riboflavin, 4.8 ; pyridoxine, 4.8 ; niacin, 23.8 ; Ca-D-pantothenate, 19 ; myo-inositol, 152 ; D-biotin,0.2 ; folic acid, 1 ; p-aminobenjoic acid, 95 ; mennadione, 1.9 ; A, 1.9 ; $D_3$, 0.4 ; choline chloride, 500 ; cyanocobalamin, 0.01. Triplicate groups of the 50 fish averaging 4.25 g were fed one of four isoproteic ($47\%$) and isolipidic ($9\%$) experimental diets to satiation twice a day for 10 weeks. Weight gain, feed efficiency and protein retention in fish fed the diet with vitamin premix-1 were significantly higher than those in fish fed the other diets (P<0.05). Moisture, protein and lipid contents of muscle and whole body were not affected by different dietary vitamin premix (P>0,05). These results indicate that premix-1 can be used to adequate supplemental vitamin premix in test diet containing fish meal as protein source for juvenile Korean rockfish.

• The Korean Journal of Physiology and Pharmacology
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• v.9 no.2
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• pp.131-135
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• 2005

Potassium channels in human skin fibroblast have been studied as a possible site of Alzheimer disease pathogenesis. Fibroblasts in Alzheimer disease show alterations in signal transduction pathway such as changes in $Ca^{2+}$ homeostasis and/or $Ca^{2+}-activated$ kinases, phosphatidylinositol cascade, protein kinase C activity, cAMP levels and absence of specific $K^+$ channel. However, little is known so far about electrophysiological and pharmacological characteristics of large-conductance $Ca^{2+}$-activated $K^+$ ($BK_{Ca}$) channel in human fibroblast (CRL-1474). In the present study, we found Iberiotoxin- and TEA-sensitive outward rectifying oscillatory current with whole-cell recordings. Single channel analysis showed large conductance $K^{+}$ channels (106 pS of chord conductance at +40 mV in physiological $K^+$ gradient). The 106 pS channels were activated by membrane potential and $[Ca^{2+}]_i$, consistent with the known properties of $BK_{Ca}$ channels. $BK_{Ca}$ channels in CRL-1474 were positively regulated by adenylate cyclase activator ($10{\mu}M$ forskolin), 8-Br-cyclic AMP ($300{\mu}M$) or 8-Br-cyclic GMP ($300{\mu}M$). These results suggest that human skin fibroblasts (CR-1474) have typical $BK_{Ca}$ channel and this channel could be modulated by c-AMP and c-GMP. The electrophysiological characteristics of fibroblasts might be used as the diagnostic clues for Alzheimer disease.

• The Korean Journal of Physiology and Pharmacology
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• v.3 no.6
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• pp.571-578
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• 1999

This study evaluated the effects of PKC activation using phorbol 12-myristate 13-acetate (PMA) and PKC inhibition using the isoquinoline sulfomide derivative H-7 on hemodynamics and glucoregulation in the isolated perfused rat liver. Livers were isolated from fed male Holtzman rats and perfused with Krebs Ringer bicarbonate solution under a constant flow of 50 ml/min at $35^{\circ}C.$ Portal vein pressure, glucose and lactate concentrations in the medium and oxygen consumption rates were continuously monitored by a Grass polygraph, YSI glucose and lactate monitors, and a YSI oxygen monitor, respectively. PMA at concentration of 2 to 200 nM increased the portal vein pressure, glucose and lactate production, but decreased oxygen consumption rate in a dose-dependent fashion. H-7 $(200\;{\mu}M)$ attenuated PMA (50 nM)-induced vasoconstriction $(15.1{\pm}1.36\;vs\;10.56{\pm}1.17\;mmHg),$ glucose production rate $(91.3{\pm}6.15\;vs\;71.8{\pm}2.50\;{\mu}moles/g/hr),$ lactate production rate $(72.4{\pm}6.82\;vs\;53.6{\pm}4.82\;{\mu}moles/g/hr)$ and oxygen consumption rate $(33.7{\pm}1.41\;vs\;27.9{\pm}1.75\;{\mu}l/g/min).$ The effects of PMA were blocked either by addition of verapamil $(9\;{\mu}M)$ or perfusion with $Ca^{2+}-free$ KRB. These results suggest that the hemodynamic and glucoregulatory changes in the perfused rat liver are mediated by protein kinase C activation and require $Ca^{2+}$ influx from the extracellular fluid.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.5
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• pp.1949-1953
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• 2014

Background: CA125 and HE4 are used in calculating Risk of Malignancy Algorithm (ROMA); and Risk of Malignancy Index (RMI). However, studies showed that normal levels of CA125, and HE4 differ among ethnicities such as between Asians and Caucasians, thus affecting the accuracy of the RMI score and ROMA in predicting ovarian malignancy. This study aimed to determine whether new or modified cutoff values for Ca125, HE4, the RMI score, and ROMA resulted in a better prediction of malignancy compared with the previous or standard ones. Materials and Methods: Serum level of CA125 and HE4 from 128 patients with diagnosis of ovarian tumor that had been collected before surgery at Cipto Mangunkusumo General Hospital (CMH) in Jakarta from November 2010 until May 2011 were reviewed and analysed. The standard cutoff values of these biomarkers, RMI, and ROMA were modified by using logistic regression model. The modified cutoff values were compared to the standard cutoff values in terms of sensitivity, specificity, and accuracy. Results: The modified cutoff value of CA125, HE4, RMI score and ROMA were 165.2 U/mL, 103.4 pM, 368.7, 28/54. The sensitivity and specificity of the modified cutoff values CA125, HE 4, RMI score and ROMA in differentiating benign from malignant and borderline were 67% and 75,4%; 73.1% and 85.2%; 73.1% and 80.3%; and 77.6% and 86.9%. While the sensitivity and specificity of the standard cutoff value of CA125; HE4; RMI score; and ROMA were 91% and 24.6%; 83.6% and 65%; 80.6% and 65.6%; and 91.0% and 42.6%. The accuracy of modified cutoff values compared with standard cutoff values were: 71.2% vs 59.3%, 78.9% vs 75% vs, 76.5% vs 73.4%, and 82% vs 67.9%. Conclusions: The new or modified cutoff values of Ca125, HE4, RMI score and ROMA resulted in higher accuracy compared to the previous or standard ones, at the cost of reduced sensitivity.

• Molecules and Cells
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• v.40 no.12
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• pp.906-915
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• 2017

Impairment of wound healing is a common problem in individuals with diabetes. Adiponectin, an adipocyte-derived cytokine, has many beneficial effects on metabolic disorders such as diabetes, obesity, hypertension, and dyslipidemia. C1q/TNF-Related Protein 9 (CTRP9), the closest paralog of adiponectin, has been reported to have beneficial effects on wound healing. In the current study, we demonstrate that CTRP9 regulates growth, differentiation, and apoptosis of HaCaT human keratinocytes. We found that CTRP9 augmented expression of transforming growth factor beta 1 ($TGF{\beta}1$) by transcription factor activator protein 1 (AP-1) binding activity and phosphorylation of p38 in a dose-dependent manner. Furthermore, siRNA-mediated suppression of $TGF{\beta}1$ reversed the increase in p38 phosphorylation induced by CTRP9. siRNA-mediated suppression of $TGF{\beta}1$ or p38 significantly abrogated the effects of CTRP9 on cell proliferation and differentiation while inducing apoptosis, implying that CTRP9 stimulates wound recovery through a $TGF{\beta}1$-dependent pathway in keratinocytes. Furthermore, intravenous injection of CTRP9 via tail vein suppressed mRNA expression of Ki67 and involucrin whereas it augmented $TGF{\beta}1$ mRNA expression and caspase 3 activity in skin of type 1 diabetes animal models. In conclusion, our results suggest that CTRP9 has suppressive effects on hyperkeratosis, providing a potentially effective therapeutic strategy for diabetic wounds.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2003.11a
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• pp.65-65
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• 2003

The aim of this study was to investigate the effect of resveratrol on the oxidative stress-induced inhibition of gap junctional intercellular communication (GJIC) in HaCaT keratinocyte. Anti-oxidative activity of resveratrol was measured by a,a-diphenyl-b-picrylhydrazyl (DPPH) assay and dichlorodihydrofluorescein diacetate oxidation assay. GJIC of HaCaT keratinocyte was assessed using the scrape loading/dye transfer technique. Western blots and reverse transcription-polymerase chain reaction were also analyzed for Connexin 43 protein and mRNA expression, respectively. Resveratrol scavenged directly the stable DPPH radical over a concentration range of 4 mg/$\mell$ (78.2 $\pm$ 2.7% of control) to 500 mg/$\mell$ (29.9 $\pm$ 4.2% of control) and prevent to increase the intracellular fluorescence induced by oxidative stress significantly. Ultraviolet A irradiation (UVA) and 12-O-tetradecanoylphorbol-13-acetate markedly reduced GJIC, which was restored by resveratrol. There were no significant differences in the level of Connexin 43 protein and mRNA expression among any of the experimental groups. Our data suggests that resveratrol has the protective effect on the oxidative stress-induced inhibition of gap junctional intercellular communication in HaCaT keratinocyte and this protection is likely due to the scavenging of reactive oxygen species.

• Journal of Nutrition and Health
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• v.31 no.9
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• pp.1468-1480
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• 1998

This study was conducted to investigate the nutritional intake of people in rural areas using 24-hour recall method. Kyungki Yeoju, Kangwon Whengsung, Chungbuk Chungju, Kyungnam Ulju, and Junbuk Jungup were selected for this study. The results were as follows 1) The mean daily energy intake was 2055.7kcal for male, 1703.2kcal for female. Fat intake were 43.0g for male, 32.7g for (female and protein intake was 74.5g for male 61.5g for female. Nutrient intake of Ulju residents were the highest and that of Whengsung and Yeoju residents were the lowest. Nutrient intake decreased significantly in elderly over 70 years. 2) Nutrients consumed below 80% of Korean RDA were Ca, Vit A, riboflavin and Vit E. Ulju residents consumed significantly higher protein, Ca, P compared to other area residents. P, Fe, Vit C intake of adults male were significantly higher than those of elderly over 80 years. Vit A, thiamin and riboflavin consumption of adults female were also significantly higher than those of elderly over 80 years. Ca, Vit A, riboflavin and Vit I were consumed below the Korean RDA in both male and female. 3) Average CPF ratio of energy intake was 69.2 : 14 : 16.8. Energy intake ratio from carbohydrate was significantly lower in Ulju residents compared to Yeoju and Jungup residents. Energy intake ratio from protein was significantly higher in Ulju area than the other areas. Carbohydrate dependency was increased with age, meanwhile fat dependency was decreased with age. 4) The mean adequacy ratio(MAR), an index of overall dietary quality, were significantly different among areas : the highest was 0.81 in Ulju, the lowest was 0.65 in Whengsung. Adults of 20-49 years showed the highest MAR of 0.76 and the lowest MAR was 0.52 in over 80 years group. The indexes of nutritional quality(INQ) was higher in 01;u area than the other areas, and INQ showed the tendency to decrease with increasing age. Especially, there were significant decrease in INQ of all nutrients except Vit A with age. Based on these results, it is evident that people in rural area did not consume enough nutrients. Specially, dietary intake of Vit A, Vit B$_2$, Vit E and Ca were not adequate. (Korean J Nutrition 31(9) : 1468-1480, 1998)