• Korean Journal of Agricultural Science
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• v.37 no.2
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• pp.245-248
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• 2010

This study was conducted to investigate effect of changes in target fat and protein contents in milk on feed cost using a simulation modeling approach based on the 2001 dairy NRC. Two simulations were done; simulation I had a limitation (up to 20%), but simulation II had no limitation for the use of cottonseed hull in a diet. Using commonly used feed ingredients in Korea, we formulated least cost diets that meet nutrient requirement of a lactating dairy cow producing 36 kg of milk with combinations of 0.1% decrease or 0.1% increase in target milk fat or protein, respectively, from the national average milk fat (4.0%) and milk protein (3.1%). The contents of alfalfa and corn in a least-cost diet were decreased and those of tall fescue, whole cottonseed and rapeseed meal were increased with decreasing fat and/or increasing protein in milk. Scenarios that decreased target milk fat percentage from 4.0% to 3.9% reduced feed cost by 2 won per kg. Due to decrease in feed intake, daily feed cost was even more reduced (136 won per head) by decreasing target milk fat percentage. Increase in target milk protein percentage from 3.1% to 3.2% reduced feed cost by 6 won per kg. Among scenarios simulated, the least feed cost was obtained in scenario aimed for 3.9% fat and 3.2% of protein in milk. We conclude that a feeding practice for increasing milk protein percentage does not directly increase feed cost. In addition, feeding practices that increase protein content in milk is expected to improve economic life-span and reproductive performance of dairy cows.

• Journal of KIISE:Computer Systems and Theory
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• v.33 no.5
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• pp.267-281
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• 2006

PPI(Protein-Protein Interaction) data has information about the organism has maintained a life with some kind of mechanism. So, it is used in study about cure research back, cause of disease, and new medicine development. This PPI data has been increased by geometric progression because high throughput methods are developed such as Yeast-two-hybrid, Mass spectrometry, and Correlated mRNA expression. So, it is impossible that a person directly manage and analyze PPI data. Fortunately, PPI data is able to abstract the graph which has proteins as nodes, interactions as edges. Consequently, Graph theory plentifully researched from the computer science until now is able to be applied to PPI data successfully. In this paper, we introduce Proteinca(PROTEin INteraction CAbaret) workbench system for easily managing, analyzing and visualizing PPI data. Proteinca assists the user understand PPI data intuitively as visualizing a PPI data in graph and provide various analytical function on graph theory. And Protenica provides a simplified visualization with gravity-rule.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.64 no.4
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• pp.373-383
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• 2019

The objectives of this study were to compare the protein expression patterns and degrees and identify the protein function of disomic addition lines (DAs) in Leymus racemosus, in order to improve the quality of wheat. Upon SDS-PAGE, L. racemosus showed two major protein bands whereas Chinese Spring (CS) had four major protein bands of high molecular weight. The DA(s) generally showed a similar protein expression pattern to that of CS, because 42 chromosomes were from CS and two chromosomes were from L. racemosus. However, only the L.r[J] line showed two protein bands of between 15 and 20 kDa, like L. racemosus. Image analysis based on 2-DE revealed that L.r[F] had the most upregulated protein spots, whereas L.r[N] had the least upregulated protein spots. For L.r[I], the frequency of the downregulated protein spots was higher than that of the upregulated ones. Using MALDI-TOF MS, the protein function was identified for each protein spot on the 2-DE polyacrylamide gel. The protein spots were classified into 11 groups according to protein function. Among the 11 groups, most protein spots of the DA(s) were identified as proteins related to metabolism. Additionally, unique protein spots of the DA(s) were related to abiotic stressors such as cold and heat. Those proteins are useful for improving wheat quality with resistance against abiotic stressors.

• The KIPS Transactions:PartB
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• v.15B no.4
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• pp.375-382
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• 2008

A protein's subcellular localization is considered an essential part of the description of its associated biomolecular phenomena. As the volume of biomolecular reports has increased, there has been a great deal of research on text mining to detect protein subcellular localization information in documents. It has been argued that linguistic information, especially syntactic information, is useful for identifying the subcellular localizations of proteins of interest. However, previous systems for detecting protein subcellular localization information used only shallow syntactic parsers, and showed poor performance. Thus, there remains a need to use a full syntactic parser and to apply deep linguistic knowledge to the analysis of text for protein subcellular localization information. In addition, we have attempted to use semantic information from the WordNet thesaurus. To improve performance in detecting protein subcellular localization information, this paper proposes a three-step method based on a full syntactic dependency parser and WordNet thesaurus. In the first step, we constructed syntactic dependency paths from each protein to its location candidate, and then converted the syntactic dependency paths into dependency trees. In the second step, we retrieved root information of the syntactic dependency trees. In the final step, we extracted syn-semantic patterns of protein subtrees and location subtrees. From the root and subtree nodes, we extracted syntactic category and syntactic direction as syntactic information, and synset offset of the WordNet thesaurus as semantic information. According to the root information and syn-semantic patterns of subtrees from the training data, we extracted (protein, localization) pairs from the test sentences. Even with no biomolecular knowledge, our method showed reasonable performance in experimental results using Medline abstract data. Our proposed method gave an F-measure of 74.53% for training data and 58.90% for test data, significantly outperforming previous methods, by 12-25%.

• Journal of Korean Home Economics Education Association
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• v.24 no.2
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• pp.51-62
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• 2012

This research examined the method and amount changes of recommended protein intakes(RPI) for male and female adult, and pregnant lactating women from 1962's Recommended Dietary Allowances for Korean(KRDA) to 2010's Dietary Reference Intakes for Koreans(KDRIs) revised. As male and female adult's RPI calculation, factorial method was applied until 1989 KRDA, after that nitrogen balance study was applied. Basal factor in factorial method was standard protein(egg or milk protein) requirement or obligatory nitrogen(protein) loss. On the other hand, basal factor in nitrogen balance study was minimum dietary protein requirement to maintain nitrogen equilibrium balance(nitrogen intake = nitrogen excretion). Adjusting factors of RPI were stress and/or protein requirement difference among people. The RPI of male adults were 50~80 g/day, that of female adults were 45~70 g/day. The additional RPI of pregnant women were 10~30 g/day, were calculate based upon the extra protein needs caused by unborn child development. The pregnant women's additional RPI of 2010's KDRIs revised in the periods of first, second, and third trimester were 0, 15, 30 g/day, respectively. The additional RPI of lactation women were 20~30 g/day, were calculated based upon the extra protein needs caused by maternal milk secretion.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.11
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• pp.1725-1733
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• 2019

Objective: Evaluate the partial replacement of soybean meal with different protein sources in piglet feed during the nursery phase in terms of digestibility of feed, nitrogen balance, growth performance and blood parameters. Methods: Experiment I involved 24 crossbred entire male pigs with an initial body weight (BW) of $18.28{\pm}0.7kg$ and used a randomized complete block design consisting of 3 treatments (fish meal, FM; soybean protein concentrate, SPC; and soybean meal, SBM) and 8 replicates, with 1 pig per experimental unit. Experiment II involved 1,843 crossbred male and female pigs with an initial BW of $6.79{\pm}0.90kg$ and was based on a completely randomized design with a $2{\times}3$ factorial arrangement (2 sexes and 3 protein sources) and 13 replicates. Results: The results of Exp. I indicate effects (p<0.05) of dietary protein sources on digestible protein (FM, 17.84%; SPC, 16.72%, and SBM, 18.13%) and on total nitrogen excretion (TNE, $g/kg\;BW^{0.75}/d$) in which pigs fed with SBM-based feed had TNE values that were 5.36% and 3.72% greater than SPC and FM, respectively. In the Exp. II, there was difference (p<0.01) between sexes in the pre-starter I and starter phases, and total period in average daily feed intake (ADFI), which were greater in females, and between the protein sources, ADFI, final weight and daily weight gain. For urea in the pre-starter II and starter phases and glucose in the pre-starter II phase, there was a difference (p<0.05) between protein sources and between sexes, in starter phase in urea concentrations (females: 57.11 mg/dL and males: 50.60 mg/dL). Conclusion: The use of SBM as only protein source influences larger TNE ($g/kg\;BW^{0.75}/d$), reduces the growth performance of piglets and increases plasma urea concentrations in prestarter II phase.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.7
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• pp.1008-1013
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• 2001

This experiment was conducted to determine the effects of enzyme supplementation on the performance of 80 growing-finishing pigs (26.2 kg) fed diets containing either soybean or canola meal. Barley-based diets formulated using either soybean meal or canola meal were fed with or without enzyme (Allzyme Vegpro, Alltech Biotechnology Centre). Eight castrates and twelve gilts were fed each diet. Digestibility of dry matter, crude protein and gross energy was 8.0 (p=0.0001), 7.9 (p=0.0005) and 7.9 (p=0.0003) percent lower for pigs fed diets containing canola meal compared with soybean meal. Enzyme supplementation had no effect on nutrient digestibility (p>0.05). There was a significant interaction between protein source and enzyme for all three nutrients. Over the entire experimental period (26.2 to 77.9 kg), pigs fed canola meal consumed 9.4% less feed (p=0.001), gained weight 20.4% slower (p=0.001) and had a 12.9% poorer feed conversion (p=0.001) than pigs fed soybean meal. Weight gain, feed intake and feed conversion were unaffected by enzyme addition (p>0.05). Castrates gained weight 11.4% faster (p=0.001), consumed 9.3% more feed (p=0.001) and had a 2.6% better feed conversion (p=0.026) than gilts. There was a significant interaction between protein source and sex of pig for feed conversion. Pigs fed diets based on canola meal had a significantly lower carcass value index (p=0.01), lower lean yield (p=0.007) and lower lean depth over the loin (p=0.001) than pigs fed diets based on soybean meal. Enzyme addition significantly increased lean depth over the loin (p=0.01). There was a significant interaction between protein source and enzyme for carcass value index (p=0.04), estimated lean yield (p=0.05) and fat depth over the loin (p=0.05). These results confirm previous studies which have demonstrated poorer pig performance when canola meal completely replaces soybean meal in diets fed to growing-finishing pigs. In addition, the results provide little justification for the inclusion of the Vegpro enzyme in diets fed to pigs of this weight range.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.1011-1018
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• 2015

This study was conducted to investigate the plasma phosphoproteome and differential plasma phosphoproteins in cases of of Opisthorchis viverrini (OV)-related cholangiocarcinoma (CCA). Plasma phosphoproteomes from CCA patients (10) and non-CCA subjects (5 each for healthy subjects and OV infection) were investigated using gel-based and solution-based LC-MS/MS. Phosphoproteins in plasma samples were enriched and analyzed by LC-MS/MS. STRAP, PANTHER, iPath, and MeV programs were applied for the identification of their functions, signaling and metabolic pathways; and for the discrimination of potential biomarkers in CCA patients and non-CCA subjects, respectively. A total of 90 and 60 plasma phosphoproteins were identified by gel-based and solution-based LC-MS/MS, respectively. Most of the phosphoproteins were cytosol proteins which play roles in several cellular processes, signaling pathways, and metabolic pathways (STRAP, PANTHER, and iPath analysis). The absence of serine/arginine repetitive matrix protein 3 (A6NNA2), tubulin tyrosine ligase-like family, member 6, and biorientation of chromosomes in cell division protein 1-like (Q8NFC6) in plasma phosphoprotein were identified as potential biomarkers for the differentiation of healthy subjects from patients with CCA and OV infection. To differentiate CCA from OV infection, the absence of both serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform and coiled-coil domain-containing protein 126 precursor (Q96EE4) were then applied. A combination of 5 phosphoproteins may new alternative choices for CCA diagnosis.

• Molecules and Cells
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• v.39 no.1
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• pp.65-71
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• 2016

A challenge in the redox field is the elucidation of the molecular mechanisms, by which $H_2O_2$ mediates signal transduction in cells. This is relevant since redox pathways are disturbed in some pathologies. The transcription factor OxyR is the $H_2O_2$ sensor in bacteria, whereas Cys-based peroxidases are involved in the perception of this oxidant in eukaryotic cells. Three possible mechanisms may be involved in $H_2O_2$ signaling that are not mutually exclusive. In the simplest pathway, $H_2O_2$ signals through direct oxidation of the signaling protein, such as a phosphatase or a transcription factor. Although signaling proteins are frequently observed in the oxidized state in biological systems, in most cases their direct oxidation by $H_2O_2$ is too slow ($10^1M^{-1}s^{-1}$ range) to outcompete Cys-based peroxidases and glutathione. In some particular cellular compartments (such as vicinity of NADPH oxidases), it is possible that a signaling protein faces extremely high $H_2O_2$ concentrations, making the direct oxidation feasible. Alternatively, high $H_2O_2$ levels can hyperoxidize peroxiredoxins leading to local building up of $H_2O_2$ that then could oxidize a signaling protein (floodgate hypothesis). In a second model, $H_2O_2$ oxidizes Cys-based peroxidases that then through thiol-disulfide reshuffling would transmit the oxidized equivalents to the signaling protein. The third model of signaling is centered on the reducing substrate of Cys-based peroxidases that in most cases is thioredoxin. Is this model, peroxiredoxins would signal by modulating the thioredoxin redox status. More kinetic data is required to allow the identification of the complex network of thiol switches.

• Food Science of Animal Resources
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• v.40 no.1
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• pp.1-10
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• 2020

Various processing methods have a great impact on the physiochemical and nutritional properties of meat that are of health concern. Hence, the postmortem processing of meat by different methods is likely to intensify the potential effects on protein oxidation. The influence of meat protein oxidation on the modulation of the systemic redox status and underlying mechanism is well known. However, the effects of processed meat proteins isolated from different sources on gut microbiota, oxidative stress biomarkers, and metabolomic markers associated with metabolic syndromes are of growing interest. The application of advanced methodological approaches based on OMICS, and mass spectrometric technologies has enabled to better understand the molecular basis of the effect of processed meat oxidation on human health and the aging process. Animal studies indicate the involvement of dietary proteins isolated from different sources on health disorders, which emphasizes the impact of processed meat protein on the richness of bacterial taxa such as (Mucispirillum, Oscillibacter), accompanied by increased expression of lipogenic genes. This review explores the most recent evidences on meat processing techniques, meat protein oxidation, underlying mechanisms, and their potential effects on nutritional value, gut microbiota composition and possible implications on human health.