• Bioinformatics and Biosystems
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• v.1 no.1
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• pp.82-87
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• 2006

The most popular protein structure prediction method is comparative modeling. To guarantee accurate comparative modeling, the sequence alignment between a query protein and a template should be accurate. Although choosing the best template based on the protein sequence alignments is most critical to perform more accurate fold-recognition in comparative modeling, even more critical is the sequence alignment quality. Contrast to a lot of attention to developing a method for choosing the best template, prediction of alignment accuracy has not gained much interest. Here, we develop a method for prediction of the shift score, a recently proposed measure for alignment quality. We apply support vector regression (SVR) to predict shift score. The alignment between a query protein and a template protein of length n in our own library is transformed into an input vector of length n +2. Structural alignments are assumed to be the best alignment, and SVR is trained to predict the shift score between structural alignment and profile-profile alignment of a query protein to a template protein. The performance is assessed by Pearson correlation coefficient. The trained SVR predicts shift score with the correlation between observed and predicted shift score of 0.80.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.47 no.3
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• pp.211-219
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• 2014

To confirm the food quality and storage stability of commercial Korean kamaboko, we experimented with the composition and textural properties using various surimis and kamaboko products. We also investigated changes in protein digestibility and lipid oxidation of vacuum packed products under chilled storage at $4{\pm}1^{\circ}C$. Among the fish meatbased surimi, vegetable mixed surimi had the lowest protein content (23.73 %), as compared to other surimi (51.9-73.6%). Siginificant (P<0.05) differences in protein, lipid content and degree of fat oxidation were noted between the fried kamaboko products of three companies. Adhesiveness, springiness, cohesiveness, gumminess, chewiness and resilience were similar in all samples, but there were notable differences in hardness and fractuability between samples. In vitro protein digestibility and trypsin indigestible substrate (TIS) were not inversely proportional in fried kamaboko products. The protein digestibility (80.30%) of steamed vegetable mixed fried kamaboko was lower than that of other fried samples (84.9-86.2%). Computed protein efficiency ratio (C-PER) of companies A and C's fried kamaboko was 2.6 but company B's was 1.9. There was no noticeable change in thiobarbituric acid reactive substances (TBARs) or protein digestibility for any of the vacuum packed fried kamaboko during 30 days of chilled storage.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.5
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• pp.598-606
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• 2010

This study investigated the nutritional quality of soybean meal (SBM) fermented by Aspergillus ($FSBM_A$) and/or followed by Lactobacillus fermentation ($FSBM_{A+L}$). Both fermented products significantly improved protein utilization of SBM with higher trichloroacetic acid (TCA) soluble true protein content, in vitro protein digestibility and available lysine content, especially in $FSBM_{A+L}$. Moreover, $FSBM_{A+L}$ produced a huge amount of lactic acid resulting in lower pH as compared to the unfermented SBM or soybean protein concentrate (SPC) (p<0.05). $FSBM_A$ and $FSBM_{A+L}$ raised 4.14% and 9.04% of essential amino acids and 5.38% and 9.37% of non-essential amino acids content, respectively. The ${\alpha}$-galactoside linkage oligosaccharides such as raffinose and stachyose content in $FSBM_A$ and $FSBM_{A+L}$ decreased significantly. The results of soluble protein fractions and distribution showed that the ratio of small protein fractions (<16 kDa) were 42.6% and 63.5% for $FSBM_A$ and $FSBM_{A+L}$, respectively, as compared to 7.2% for SBM, where the ratio of large size fractions (>55 kDa, mainly ${\beta}$-conglycinin) decreased to 9.4%, 5.4% and increased to 38.8%, respectively. There were no significant differences in ileal protein digestibility regardless of treatment groups. SPC inclusion in the diet showed a better protein digestibility than the SBM diet. In summary, soybean meal fermented by Aspergillus, especially through the consequent Lactobacillus fermentation, could increase the nutritional value as compared with unfermented SBM and is compatible with SPC.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.39 no.3
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• pp.278-284
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• 1994

The sulfur amino acid composition in soybean (Glycine max L.) seeds may be an essential characteristic of new cultivars for some animal diets. Variation in seed storage protein among genotypes might make it possible to improve the quality of seed protein by genetically altering seed storage protein composition through plant breeding. This study was carried out to determine if mutant strains have potential for improving seed protein quality in soybean. Ten mutant strains had a distinct characteristic of seed storage protein subunits. Among the mutant strains, the sulfur amino acid compositions(methionine plus cystein) of Keburi(P.I.417016), Keburi(P.I.506817), and P.I.54608-1 were relatively higher than those of the others and were 1.9, 2.1, and 1.8%, repectively, which might be due to low levels of ${\alpha}$, ${\alpha}$', and ${\beta}$ subunits of 7S protein. Therefore, it is concluded that the mutant strains, Keburi(P.I.417016), Keburi(P.I.506817), and P.I.54608-1 appear to be potential materials for a breeding program for improving sulfur amino acid composition, and the others also seem to be possible breeding materials for other uses.

• Journal of Environmental Science International
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• v.5 no.5
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• pp.643-656
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• 1996

Various light intensity and light quality were treated to oat seedlings to investigate the effect of light on the chlorophyll accumulation and the formation of chlorophyll-protein complexes. The Increase of total chlorophyll accumulation and Chl (chlorophyll) a/b ratio was promoted under H (high intensity) white light during oat chloroplast development when compared to 1 (low intensity) white light. Also H white light was more effective in the formation of chlorophyll-protein complexes associated with PSI CCI and CCII than L white light. The seedlings grown in various right quality caused little changes in total chiorophyl and ChI-a/b ratio when compared to those grown in L white light. The assembly of LHCII trimer was more affected by L white light treatment in the formation of-chlorophyll-protein complexes than red light treatment. The effect of blue light on the relative composition of chlorophyll-protein complexes was similar to that of L white light. Particualrly, blue light was more effective in the synthesis of LHCII monomer than the other light quality at the early stage of greening. When compared to red light, blue light was more effective the increase of chlorophyll accumulation and Chl a/b ratio than 1ight Quality, and light Quality may be in important factor for the regulation of the organization in the chlorophyll-protein complexes curing greening.

• Preventive Nutrition and Food Science
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• v.3 no.3
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• pp.241-247
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• 1998

Fish extracts were processed at high temperature (136.7 ~14$0^{\circ}C$) for possible use as functional food ingredients. Raw fish meats and those hydrothermal extracts were compared with respect to in vitro and in vivo protein qualities. 95% of fat inraw meats was reduced in extracts but there were not remarkable changes in other macronutrients in freeze-dried extracts. Most of essential amino acids were decreased significantly but two times more proline and glycine were detected in extracts. High temperature cooking resulted 2.1 ~3.7 times of higher total free amino acid content infish extracts compared iwth raw meat, and taurine and glutamic acid were increased especially. Severe protein damages were occurred when invitro protein quality indices such as availblae lysine, hydrophilic browing, trypsin inhibitor formation and in vitro protein digestibility were measured on fish extracts. In vivo protein qualities were also strongly influenced by high temperature ; however rat-body-weight gain was nearly zero during PER assay, and rat PER or NPR of fish extracts were significantly lower (p<0.001) than those of cotnrol (ANRC casein) and original raw fish meats.

• Asian-Australasian Journal of Animal Sciences
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• v.4 no.4
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• pp.383-393
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• 1991

The present study was carried out to investigate the effect of cimaterol on growth performance, carcass quality and cellular functional activity of broilers as affected by the various protein and energy levels. In starter period (0-21 days) all chicks were fed the basal diet which contained approximately 23 % crude protein and 3200 kcal of metabolizable energy per kg of diet. The cimaterol was added during 22-49 days and during the period of 8th week the cimaterol was withdrawn. In finisher period (22-49 days), a $2{\times}2{\times}3$ factorial arrangement consisting of 2 levels of cimaterol (0 mg/kg, 0.25 mg/kg), 2 levels of protein (19%, 17%) and 3 levels of energy (3200, 2900, 2600 kcal/kg) was used. In the finisher period, the body weight gain and feed efficiency was improved by the supplementation of cimaterol. The high protein and high energy level with supplementation of cimaterol had showed the highest body weight gain and feed efficiency, without significant difference. The administration of cimaterol had no effects on percentage of abdominal fat content, giblet and neck. Eventhough the difference was not significant (p>0.05), carcass yield was improved slightly by the administration of cimaterol. The effect of cimaterol on carcass composition was clearly demonstrated that protein content of broilers was not increased (p>0.05) but fat content decreased significantly (p<0.05). The ultilization of nutrients in experimental diets was not significantly affected by feeding cimaterol compared to control group. The results of in vitro studies with liver and adipose tissue showed that cimaterol increased the lipolytic activities at 19% protein level whereas at 17% protein level this effect was variable. Lipogenic activities in liver and adipose tissue were not affected with the administration of cimaterol but the activities increased as energy decreased, particularly in liver tissue. In cell studies with acinar culture of liver tissues, cimaterol had no effect on protein synthetic activity but the parameter was increased at higher level of dietary protein and energy. Protein secretion in liver was increased by the supplementation of cimaterol. In addition, at high protein level the protein secretion was increased and has shown the highest values at medium energy level.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.2
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• pp.254-265
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• 2002

Soybean meal (SBM) is a major protein source in poultry feeds and one of the best quality ingredients because of the relatively high protein content, good amino acid profile and bioavailability. But soybean meal quality is largely dependent on the processing technology and origins. In this experiment, effects of three different soybean meals were evaluated in layer (experiment 1) and broiler (experiment 2). Soybean meal sources used in the experiments were the US-originated dehulled soybean meal (USDHSBM), India-originated non-dehulled soybean meal (India SBM) and Brazil-originated non-dehulled soybean meal (Brazil SBM). Experiment 1 was conducted during growing and laying periods and evaluated the interactive effects of soybean meal sources according to feeding periods on growth performance and egg quality. Experiment 2 was conducted during growing period (day 1-35) and finishing period (day 35-42). The growth performance was measured for the same periods and any possible interaction between soybean meal origins and crude protein levels was also studied. In experiment 1, chicks fed India SBM utilized feed more efficiently (p<0.05) than those fed Brazil SBM from day 29 to day 42. The body weights of layers during the laying period had no relation to egg production. But egg weights were significantly heavier in all the USDHSBM fed groups than other groups (p<0.001) and depended on feed protein source during growing period (p<0.001). The average egg weight of the USDHSBM fed group scored the highest value (65.4 g), followed by the Brazil SBM fed group (62.1 g) and India SBM fed group (62.1 g). There was an effect of interaction between origins of soybean meal fed group in growing and laying period on eggshell color (p<0.01). Eggshell was significantly stronger in the USDHSBM fed (for growing period) groups than other groups (p<0.05) on $31^{st}$ week. Haugh's unit (HU), albumin index and yolk index of the USDHSBM fed group in growing stage were significantly superior (p<0.001) to other groups. In experiment 2, for the 7-week, chicks on the India SBM group gained less (p<0.001) weight than other groups. While daily gain of India SBM chicks was not affected by dietary crude protein level, those of the USDHSBM and Brazil SBM chicks were linearly increased as dietary crude protein level increased from 18% to 20%. The gain per feed ratio of the USDHSBM group was the highest (0.585), followed by the Brazil SBM group (0.568) and India SBM group (0.550) (p<0.01). Therefore, in this experiment, the use of USDHSBM with excellent protein quality and amino acid digestibility could be of advantage to the economic production of layer and broiler.

• Animal Bioscience
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• v.35 no.10
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• pp.1556-1565
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• 2022

Objective: Tan lambs (n = 36, 3 mo old, 19.1±0.53 kg) were used to assess effects of dietary guanidinoacetic acid (GAA) and rumen-protected methionine (RPM) on growth performance, carcass traits, meat quality, and serum parameters. Methods: Lambs were randomly assigned to three treatment groups, with 6 pens per group and 2 lambs per pen. Dietary treatments were: basal diet alone (I); basal diet supplemented with 0.08% GAA+0.06% RPM (II); and basal diet supplemented with 0.08% GAA+0.08% RPM (III). Diets were provided three times a day for 90 d. Intake per pen was recorded daily and individual lamb body weight (BW) was measured monthly. Carcass traits were measured after slaughter and meat quality at the end of the experiment, blood samples were taken on a subgroup of lambs for analysis of indicators mostly related to protein metabolism. Results: Final BW and average daily gain for the first and second month, and for the entire experiment were greater in Treatment II compared to Treatment I (p<0.05), whereas feed to gain ratio was lower (p<0.05). Treatment II had the optimal dressing percentage and net meat weight proportion, as well as crude protein and intramuscular fat concentrations in muscles. Treatment II improved meat quality, as indicated by the greater water holding capacity, pH after 45 min and 48 h, and lower shear force and cooking loss. Dietary supplementation of GAA and RPM also increased the meat color a^* and b^* values at 24 h. Finally, Treatment II increased total protein, and serum concentrations of albumin and creatinine, but decreased serum urea nitrogen concentrations, indicating improved protein efficiency. Conclusion: In this study, 0.08% GAA+0.06% RPM supplementation improved growth performance and meat quality of Tan lambs.

• Food Science and Biotechnology
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• v.17 no.1
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• pp.66-71
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• 2008

A total of 284 milled rice (MR) marketed in Korea were analyzed for grading characteristics (head rice, broken kernels, chalky kernels, and damaged kernels%), color characteristics (L-, a-, b-values, and whiteness), protein content (%), and the cooked rice (CR) sensory quality to investigate the key characteristics affecting the overall sensory quality of rice marketed in Korea. Relatively high correlation with the overall sensory quality of the CR was found in color characteristics such b-value of the CR (r=-0.779) and MR (r=-0.545), the a-value of the CR (r=0.513), and the whiteness (r=0.298) of the MR, compared to protein (r=-0.150), and the moisture (r=0.158) contents of the MR and the percentage of head rice (r=0.195). Partial least squares (PLS) regression of the CR b-value with various characteristics of the MR showed that CR b-value was increased with MR b-value effectively, followed by protein content, damaged kernels, chalky kernels, and colored kernels of MR while it was decreased with whiteness and moisture content for the MR.