• Journal of Life Science
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• v.28 no.9
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• pp.1007-1015
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• 2018

The E6-associated protein (E6AP) is known to induce the ubiquitination and proteasomal degradation of HCV core protein and thereby directly impair capsid assembly, resulting in a decline in HCV replication. To counteract this anti-viral host defense system, HCV core protein has evolved a strategy to inhibit E6AP expression via DNA methylation. In the present study, we further explored the mechanism by which HCV core protein inhibits E6AP expression. HCV core protein upregulated both the protein levels and enzyme activities of DNA methyltransferase 1 (DNMT1), DNMT3a, and DNMT3b to inhibit E6AP expression via promoter hypermethylation in HepG2 cells but not in Hep3B cells, which do not express p53. Interestingly, p53 overexpression alone in Hep3B cells was sufficient to activate DNMTs in the absence of HCV core protein and thereby inhibit E6AP expression via promoter hypermethylation. In addition, upregulation of p53 was absolutely required for the HCV core protein to inhibit E6AP expression via promoter hypermethylation, as evidenced by both p53 knockdown and ectopic expression experiments. Accordingly, levels of the ubiquitinated forms of HCV core protein were lower in HepG2 cells than in Hep3B cells. Based on these observations, we conclude that HCV core protein evades ubiquitin-dependent proteasomal degradation in a p53-dependent manner.

• Bulletin of the Korean Chemical Society
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• v.31 no.2
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• pp.275-280
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• 2010

Actinobacillus actinomycetemcomitans is a gram-negative, nonmotile coccobacillus bacterium that is associated with several human diseases, including endocarditis, meningitis, osteomyelitis, subcutaneous abscesses and periodontal diseases. A full-length Omp1-like protein gene from A. actinomycetemcomitans was cloned into a pQE30 vector and overexpressed in Escherichia coli BL21(DE3) cells. The protein revealed sequence homologies to Seventeen kilodalton proteins (Skp) from Pasteurella multocida and E. coli that have been characterized as periplasmic chaperones. This soluble Omp1-like protein was successfully purified to homogeneity for further folding and functional studies. The purity, identity, and conformation of the protein were determined using sodium dodecyl sulfate polyacrylamide gel electrophoresis, matrix-assisted laser desorption ionization mass spectrometry, circular dichroism, fluorescence spectroscopic, and differential scanning calorimetric studies. We showed that the protein formed an oligomer larger than a tetramer. We found, further, that it is comprised of mostly $\alpha$-helices and boasts high thermal stability.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.30 no.7 s.250
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• pp.841-848
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• 2006

Many researchers are developing computational prediction methods for protein tertiary structures to get much more information of protein. These methods are very attractive on the aspects of breaking technologies of computer hardware and simulation software. One of the computational methods for the prediction is a fragment assembly method which shows good ab initio predictions at several cases. There are many barriers, however, in conventional fragment assembly methods. Argues on protein energy functions and global optimization to predict the structures are in progress fer example. In this study, a new prediction method for protein structures is proposed. The proposed method mainly consists of two parts. The first one is a fragment assembly which uses very shot fragments of representative proteins and produces a prototype of a given sequence query of amino acids. The second one is a global optimization which folds the prototype and makes the only protein structure. The goodness of the proposed method is shown through numerical experiments.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.10
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• pp.1475-1481
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• 2003

The aim of this paper was to use the Cornell Net Carbohydrate and Protein System (CNCPS), that reports diet energy and protein value and animal requirements, as net energy for lactation ($NE_1$) and metabolizable protein (MP) respectively, to evaluate some rations for lactating Italian Mediterranean buffaloes. The investigation was carried out on six farms in the province of Caserta (southern Italy), where the milk production was controlled four times monthly on 10 animals (changing every time) chosen at different lactation days (5 categories): <2 months (A), 2-4 months (B), 4-6 months (C), 6-8 months (D), >8 months (E). Milk fat and protein were determined. Diet $NE_1$ and MP were estimated with the CPM-Dairy program (1998) using diet component chemical characteristics; then energy and protein intakes were estimated. $NE_1$ and MP requirements were estimated with two methods: 1) using CPM-Dairy that considers produced milk, fat and protein content, lactation phase and body condition score as main factors; 2) by applying the theory that to produce 1 kg of energy corrected milk, the buffalo needs 3.56 MJ of $NE_1$ and the efficiency to convert the absorbed aminoacids into milk protein is lower than cow (CNCPS). As regards energy, with method 1 the requirements were satisfactory starting from category A (4 out of 6 farms) and category B (5/6 farms); however, a surplus resulted for category E (5/6 farms). With method 2 a deficit in category A (5/6 farms) and B (3/6 farms) was observed, while the energy requirements were satisfied for all categories except E, where on only one buffalo farm had a surplus of energy intake. As regards protein, with method 1 the requirements were substantially satisfied for all the categories except E (3/6 farms); with method 2 the MP trend was much less favourable than with method 1. Indeed, a protein deficit was observed for all animals in categories A and B (5/6 farms). Moreover, on one farm the protein intake never satisfied animal requirements. In our experimental conditions, the use of the CNCPS to characterise diets for lactating buffalo and to calculate their requirements led to satisfactory results. By contrast, we cannot say the same for method 2, which applies a lower use efficiency of NE and MP for lactation in buffalo compared to cow.

• Korean Journal of Microbiology
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• v.19 no.1
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• pp.14-22
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• 1981

Protein content of cellulosic wastes, such as spent grain, hop bark, spent rye, rice straw, rice hull, saw dust and used newspaper, was increased by a mixed culture of C. utilis wastes having 66-75% moisture. Among the fungal strains tested. A.phoenicis KU175 was the most powerful to increase the protein content of A. phoenicis during the mixed culture with C. utilis in the CMC medium reached at the peak for one day culture after inoculation of the both strains at the same time, while it reached at peark from the beginning of the mixed culture, when A. phoenicis was inocultated for 12-24hours prior to the inoculation of C.utilis. To increase the protein content of the cellulosic wastes by the mixed culture of C.utilis and A.phoenicis, the inoculation of both strains at the same time was more effective than the preinoculation of A. phoenicis for 6-24 hours. Content of crude cellulose in the used newspaper, saw dust and spent grain was high relatively, and the lignin content of spent grain, spent rye, and rice strew was reduced more than half by the treatment of 2% NaOH. However, effect of alkali treatment of increase the protein content of the cellulosic wastes was not prominent in the case of mixed culture. Protein content of the cellulosic wastes was increased prominently by the mixed culture of C.utilis and A.phoenicis in semi-solid substrate, compared with the single culture of C. utilis, although the latter increased the protein content of cellulosic wastes considerably. The effect of mixed culture of C. utilis and A. phoenicis increased 4-fold the protein content of spent grain, and more than doubled crude protein in hop bark and rice straw.

• Journal of the Korean Society of Food Science and Nutrition
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• v.22 no.1
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• pp.15-18
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• 1993

To evaluate an effect of dietary protein on the intoxication of methanethiol in rats, the methanethiol was intraperitoneally injected to the rats fed a low or high protein diet and then the liver weight per body weight and seurm levels of alanine aminotransferase (ALT) activities were determined to investigate the differences in liver damage between the animal groups fed low protein diet and that fed high protein diet. On the other hand, the hepatic glutathione content and its conjugating enzyme, glutathione S-transferase (GST) activity were determined to clarify the cause of difference in liver function between the two groups. The increasing rate of liver weigh/body wt., serum levels of ALT to its control group were higher in methanethiol-treated rats fed low protein diet than those fed high protein diet. The hepatic content of glutathione and GST activity were higher in rats fed high protein diet than those fed low protein diet and the decreasing rate of hepatic glu-tathione content to its control group was higher in rats fed low protein diet than those fed high protein diet. Furthermore, the hepatic GST activity in methanethiol-treated rats was higher in rats fed high protein diet than those fed low protein diet. In case of control group, the GST activity was also higher in rats fed high protein diet than those fed low protein diet.

• Fisheries and Aquatic Sciences
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• v.7 no.4
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• pp.184-191
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• 2004

A 25-week feeding trial of two dietary protein (47 and $52\%$) and three dietary lipid level (7, 12 and $17\%$) factorial design with three replications were conducted to determine effects of dietary protein and lipid levels on growth, feed utilization and body composition of adult starry flounder (Platichthys stellatus), average initial weight 332 g, during the winter season. Survival of fish was not affected by either dietary protein or dietary lipid level. Weight gain, feed efficiency and protein efficiency ratio improved with dietary protein and lipid levels except for those of fish fed the $52\%$ protein diet with $17\%$ lipid. The best growth and feed utilization were observed in the $52\%$ protein diet with $12\%$ lipid, but were not significantly different from those of fish fed the $52\%$ protein diet with $17\%$ lipid or the $47\%$ protein diets with $17\%$ lipid levels. Hepatosomatic and visceral somatic indexes were significantly influenced by dietary protein level, but not by dietary lipid level. None of moisture, crude protein, crude lipid, or glycogen contents of dorsal muscle or liver in starry flounder except for crude lipid in dorsal muscle was significantly influenced by either dietary protein or dietary lipid level. Plasma cholesterol concentration was significantly influenced by both dietary protein and dietary lipid levels. The results of this study suggest that the diets containing $47\%$ protein with $17\%$ lipid or $52\%$ protein with $12-17\%$ lipid are optimal for growth and feed utilization of adult starry flounder under these experimental conditions.

• Molecules and Cells
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• v.27 no.3
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• pp.271-277
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• 2009

Proteins interact with each other within a cell, and those interactions give rise to the biological function and dynamical behavior of cellular systems. Generally, the protein interactions are temporal, spatial, or condition dependent in a specific cell, where only a small part of interactions usually take place under certain conditions. Recently, although a large amount of protein interaction data have been collected by high-throughput technologies, the interactions are recorded or summarized under various or different conditions and therefore cannot be directly used to identify signaling pathways or active networks, which are believed to work in specific cells under specific conditions. However, protein interactions activated under specific conditions may give hints to the biological process underlying corresponding phenotypes. In particular, responsive functional modules consist of protein interactions activated under specific conditions can provide insight into the mechanism underlying biological systems, e.g. protein interaction subnetworks found for certain diseases rather than normal conditions may help to discover potential biomarkers. From computational viewpoint, identifying responsive functional modules can be formulated as an optimization problem. Therefore, efficient computational methods for extracting responsive functional modules are strongly demanded due to the NP-hard nature of such a combinatorial problem. In this review, we first report recent advances in development of computational methods for extracting responsive functional modules or active pathways from protein interaction network and microarray data. Then from computational aspect, we discuss remaining obstacles and perspectives for this attractive and challenging topic in the area of systems biology.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.5
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• pp.675-681
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• 2002

Among Italian buffalo farmers, it is widely held that administering diets with high energy and protein concentrations is an effective way to increase milk production. In order to assess the validity of this opinion, we verified milk yield and physico-chemical characteristics from buffaloes that, from the $5^{th}$ month of lactation, were fed two total mixed rations (TMRs) which, given the same intake, should have led to satisfaction of protein requirements though with a slight energy deficit (diet A) or excessive amounts of energy and protein (diet B). Estimate of the energy and protein value of the diets and that of the corresponding requirements was carried out both by using two software programs derived from the Cornell Net Carbohydrate and Protein System (1992), and with the method set up by INRA researchers (1988). The results obtained show that the two diets administered did not result in significant changes to the quantity of milk produced. However, with Diet B the protein concentration in the milk was significantly (p<0.01) higher, although this was partly offset by the higher concentration (p<0.05) of non-protein nitrogen (NNP). The Group B buffaloes also showed significantly higher blood urea levels (p<0.01), with concentrations exceeding those considered physiological for lactating buffaloes. Finally, while administering Diet A the Body Condition Score (BCS) was close to 6.5 (Wagner et al., 1988), whereas in buffaloes which used Diet B it sometimes increased by over 0.5 points. As regards which of the two methods compared is more suitable for expressing dietary energy and protein value and corresponding requirements, we feel that due to the high variability in the Italian Mediterranean buffalo's milk production aptitude, it would be premature to express a judgement on methods which rest on a common scientific base and do not differ substantially.

• Journal of Plant Biology
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• v.35 no.1
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• pp.45-51
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• 1992

The changes of protein bodies in endosperm cells of both seeds with red seed coat and indehiscent seeds of Panax ginseng C.A. Meyer have been investigated in relation to the embryo development. In the early stage of seeds with red seed coat, spherical spherosomes were distributed in endosperm cells. Protein bodies were formed from vacuoles containing the storage protein. Cell organelles were hardly observed in the cytoplasm. In the late stage of the seed with red seed coat, the endosperm was filled with spherosomes and protein bodies. The protein bodies consisted of amorphous inclusions with high electron density or proteinaceous matrix with even electron density. In the seed of in dehiscence, the protein body in endosperm cells contained globoids and protein crystalloids. The globoid of protein body had a electron dense materials. Umbiliform layer was formed between embryo and endosperm. The deformation patterns of endosperm cell wall and the cellulose microfibril were observed in endosperm cells near the umbiliform layer. Umbiliform layer consisted of lipid body and autolyzed cell debris. The protein body of endosperm cell near the umbiliform layer showed various degenerative patterns, and so electron density of proteinaceous matrix was gradually decreased.reased.