• Journal of the Korea Institute of Information and Communication Engineering
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• v.22 no.1
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• pp.26-32
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• 2018

The protein secondary structures are important information for studying the evolution, structure and function of proteins. Recently, deep learning methods have been actively applied to predict the secondary structure of proteins using only protein sequence information. In these methods, widely used input features are protein profiles transformed from protein sequences. In this paper, to obtain an effective protein profiles, protein profiles were constructed using protein sequence search methods such as PSI-BLAST and HHblits. We adjust the similarity threshold for determining the homologous protein sequence used in constructing the protein profile and the number of iterations of the profile construction using the homologous sequence information. We used the protein profiles as inputs to convolutional neural networks and recurrent neural networks to predict the secondary structures. The protein profile that was created by adding evolutionary information only once was effective.

• Korean Journal of Veterinary Research
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• v.50 no.4
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• pp.285-295
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• 2010

Protein expression patterns in Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) strains with diverse phenotypes, such as phage type, antibiotic resistance pattern and plasmid profiles were examined. For detailed analysis of proteins expressed by different S. Typhimurium strains, protein fractions were divided into detergent-rich phase (DP) and aqueous phase (AP) using triton X-114 detergent. The two phases were subjected to two-dimensional gel electrophoresis (2-DE), followed by protein identification using peptide mass fingerprinting (PMF). In the results, PMF showed that DP fractions consisted mainly of outer membrane proteins, whereas the AP fractions included cytosolic proteins. Comparison of 2-DE profiles of DP did not show any distinct protein spots which could be correlated with phage type, antibiotic resistance pattern or plasmid profile. However, comparisons of 2-DE profiles of the AP revealed differences in the protein spots, which could be correlated with the plasmid profile and phage types. Among these protein spots, flagellin was specific for strains containing a 90 kb plasmid. Compared to DT193 phage type, three protein spots in the range of pI 5.0-5.5 and MW 8-15 kDa of AP 2-DE profiles were absent in the DT104 phage types. Additionally, a protein spot with PI in the range of 4.5-5.0 and molecular weight (MW) between 51-69 kDa was specific for phage type DT104, while a protein spot with pI in the range of 4.0-4.8 and MW between 18-20 kDa was specific for DT193 phage type. These protein spots may be useful for discriminating phage types of S. Typhimurium.

• Animal Bioscience
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• v.36 no.8
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• pp.1190-1198
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• 2023

Objective: To our knowledge, there are few studies on the correlation between internal structure of fermented products and nutrient delivery from by-products from coffee processing in the ruminant system. The objective of this project was to use advanced mid-infrared vibrational spectroscopic technique (ATR-FT/IR) to reveal interactive correlation between protein internal structure and ruminant-relevant protein and energy metabolic profiles of by-products from coffee processing affected by added-microorganism fermentation duration. Methods: The by-products from coffee processing were fermented using commercial fermentation product, called Saus Burger Pakan, consisting of various microorganisms: cellulolytic, lactic acid, amylolytic, proteolytic, and xylanolytic microbes, for 0, 7, 14, 21, and 28 days. Protein chemical profiles, Cornell Net Carbohydrate and Protein System crude protein and CHO subfractions, and ruminal degradation and intestinal digestion of protein were evaluated. The attenuated total reflectance-Ft/IR (ATR-FTIR) spectroscopy was used to study protein structural features of spectra that were affected by added microorganism fermentation duration. The molecular spectral analyses were carried using OMNIC software. Molecular spectral analysis parameters in fermented and non-fermented by-products from coffee processing included: Amide I area (AIA), Amide II (AIIA) area, Amide I heigh (AIH), Amide II height (AIIH), α-helix height (αH), β-sheet height (βH), AIA to AIIA ratio, AIH to AIIH ratio, and αH to βH ratio. The relationship between protein structure spectral profiles of by-products from coffee processing and protein related metabolic features in ruminant were also investigated. Results: Fermentation decreased rumen degradable protein and increased rumen undegradable protein of by-products from coffee processing (p<0.05), indicating more protein entering from rumen to the small intestine for animal use. The fermentation duration significantly impacted (p<0.05) protein structure spectral features. Fermentation tended to increase (p<0.10) AIA and AIH as well as β-sheet height which all are significantly related to the protein level. Conclusion: Protein structure spectral profiles of by-product form coffee processing could be utilized as potential evaluators to estimate protein related chemical profile and protein metabolic characteristics in ruminant system.

• Nutritional Sciences
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• v.5 no.2
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• pp.53-59
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• 2002

This study was conducted to examine the effects of dietary sources of fatty acids and protein on serum protein profiles, hepatic functional enzyme activities, mammary tumor incidence and tumor weight in 7, 12-dimethylbenz($\alpha$)anthracene (DMBA)-treated rats. The sources of dietary fatty acids were 18n6 (rich in linoleic acid), 18n3 (rich in linolenic acid) and 22n3 (rich in DHA) : sources of dietary protein were casein (C) and soy protein isolate (S). mammary tumors (MTs) were chemically induced by DMBA (9 mg/100 g body weight) which was gastrically intubated at 7 weeks of age. Each experimental diet was given for the following 25 weeks. Casein-fed rats (group C) exhibited significantly higher levels of weight gain and FER (food efficiency ratio) than did group S. Group C showed higher levels of serum protein and globulin, and higher albumin/globulin (A/G) ratios than group S. Liver functional enzyme activities (GOT, GPT, ALP, LDH, $\gamma$-GT) and LDH/GOT ratios were not influenced by dietary protein. GPT activity was lower in the group given 18n3, and ALP activity was lower in the group given 18n6. The incidence and total number of MTs appeared to be lower in the group given 22n3 than in the group given 18n3 or 18n6, even though the average weight of MTs was highest in the group given 22n3, The average weight of MTs was higher in the C group than in the S group. MT incidence had a positive correlation with LDH activity and LDH/GOT ratio. The average weight of MTs had a negative correlation with serum albumin levels and A/G ratios, and a positive correlation with ALP activity. This research suggests that the measurement of serum protein profiles and liver functional enzyme activities may be utilized to monitor the development of mammary tumors.

• Proceedings of the KSCN Conference
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• 2004.05a
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• pp.437.2-438
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• 2004

The purpose of this study was to investigate the effects of garlic, soy protein and taurine on blood lipid profiles in postmenopausal hyperlipidemic model rats. Seventy-two female Sprague-Dawley rats weighing 200g were fed a commercial diet for one week. All rats were ovariectomized and then were randomly assigned to eight groups (high fat diet group; HFD group, 2% garlic powder group; GP group, taurine group; TR group, soy protein group; SP group, 2% garlic powder ＋ taurine group; GP＋TR group, 2% garlic powder+ soy protein group; GP＋SP group, taurine＋soy protein group; TR＋SP group, 2% garlic powder＋taurine＋soy protein group; GP＋TR＋SP group).(omitted)

• Journal of Life Science
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• v.22 no.1
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• pp.92-97
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• 2012

The purpose of this study was to analyze the effects of aerobic exercise and a protein diet on serum lipid profiles, liver function, and immunoglobulin levels in rats. The subjects, 24 male Sprague-Dawley rats, were grouped into an exercise with protein diet group (A, n=6), a protein diet group (B, n=6), an exercise group (C, n=6), and a control group (D, n=6). The exercise with protein group trained for 4 weeks (20-30 min/day, speed at 14~17 m/min) and was given a 40% protein diet for 4 weeks. The variables of serum lipid profiles, liver function, and immunoglobulin levels were measured in all of the subjects at the end of the 4 weeks of treadmill exercise. Serum TC and LDL-C levels were significantly decreased in the exercise with protein diet group compared to the other groups and serum HDL-C, GOP, and IgG were significantly higher than in the other groups. However, no significant differences were found for the IgA and IgM levels. In conclusion, aerobic exercise with a protein diet was effective in improving serum lipid profiles, liver function, and immunoglobulin.

• Preventive Nutrition and Food Science
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• v.12 no.2
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• pp.103-110
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• 2007

The protein profiles among Korean rice cultivars were assessed by total protein determination, solubility fractionation, SDS-PAGE analysis and scanning densitometry. In the extraction of protein, the SDS/urea system at a neutral pH was more efficient than that at alkaline pH. The determination of total protein showed that the protein content was similar among cultivars, ranging from 87.9 to 92.7 mg/g dry weight. Additionally, the water/NaCl-soluble protein fraction, containing 14${\sim}$16 kDa albumin and 22 kDa globulin ${\alpha}$-globulin, was also similar among cultivars, with a range of 9.94 to 11.98 mg/g dry weight. The SDS-PAGE/densitometry of total protein showed that there was no discernable difference in proteins of higher molecular weights among various cultivars, whereas the amount of lower molecular weight proteins (14${\sim}$16 kDa) is somewhat variable among cultivars. Furthermore, SDS-PAGE analysis of water/NaCl-soluble and propanol-soluble fractions indicates that there is a discernible change in the content of albumin, globulin or prolamin among cultivars. Thus, the PAGE/densitometry method, preceded by solubility fractionation, is useful for examining differences in protein profiles of rice cultivars.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.2
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• pp.236-244
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• 2006

This study was designed to determine the effects of daidzein (DE) on hepatic lipid metabolism in chicks fed with low protein (LP) diet based on casein. In experiment 1, the male chicks were fed with one of the three levels of dietary protein containing 10.95%, 21.9% and 43.8% protein content for 2 days. In experiment 2, the chicks were fed one of the three levels of protein with or without DE at 1,000 mg/kg diet for 2 days. Experiment 3 was conducted to compare DE (LP+DE) with estradiol (LP+E2) in chicks fed with LP diet for 7 days. Plasma lipid profiles, hepatic lipid profiles, activities of hepatic malic enzyme and isocitrate dehydrogenase (ICDH) were measured. Transcriptions of hepatic fatty acid synthase, apolipoprotein-B (APO-B), and fructose bisphosphatase mRNA were measured by RT-PCR. Increasing dietary protein levels markedly decreased the concentrations of plasma triglycerides, hepatic total lipids, hepatic TG, and the mRNA transcriptions while the increased dietary protein levels increased hepatic ICDH activities in experiment 1. In experiment 2, the effects of dietary protein levels on blood and hepatic lipid content were more prominent than those of the additional DE. Interestingly, plasma TG levels were affected by DE supplementation (p<0.05). In experiment 3, DE inhibited APO-B mRNA expressions and stimulated the accumulation of lipid in the liver through mechanisms different from E2. In this study, we demonstrate that DE has beneficial effects on blood lipid profiles, but that it inhibits APO-B mRNA transcription and aggravates the fatty liver induced by LP diet in chicks.

• Journal of Korean Neurosurgical Society
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• v.59 no.6
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• pp.570-576
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• 2016

Objective : Elevated cell counts and protein levels in cerebrospinal fluid (CSF) result from disease activity in patients with leptomeningeal carcinomatosis (LMC). Previous studies evaluated the use of CSF profiles to monitor a treatment response or predict prognosis. CSF profiles vary, however, according to the sampling site and the patient's systemic condition. We compared lumbar and ventricular CSF profiles collected before intraventricular chemotherapy for LMC and evaluated the association of these profiles with patients' systemic factors and LMC disease activity. Methods : CSF profiles were retrospectively collected from 228 patients who underwent Ommaya reservoir insertion for intraventricular chemotherapy after a diagnosis of LMC. Lumbar samples taken via lumbar puncture were used for the diagnosis, and ventricular samples were obtained later at the time of Ommaya reservoir insertion. LMC disease activity was defined as the presence of LMC-related symptoms such as increased intracranial pressure, hydrocephalus, cranial neuropathy, and cauda equina syndrome. Results : Cell counts (median : 8 vs. 1 cells/mL) and protein levels (median : 68 vs. 17 mg/dL) significantly higher in lumbar CSF than in ventricular CSF (p<0.001). Among the evaluated systemic factors, concomitant brain metastasis and previous radiation were significantly correlated with higher protein levels in the lumbar CSF (p=0.01 and <0.001, respectively). Among the LMC disease activity, patients presenting with hydrocephalus or cauda equina syndrome showed higher lumbar CSF protein level compared with that in patients without those symptoms (p=0.049 and p<0.001, respectively). The lumbar CSF cell count was significantly lower in patients with cranial neuropathy (p=0.046). The ventricular CSF cell counts and protein levels showed no correlation with LMC symptoms. Carcinoembryonic antigen (CEA), which was measured from ventricular CSF after the diagnosis in 109 patients, showed a significant association with the presence of hydrocephalus (p=0.01). Conclusion : The protein level in lumbar CSF indicated the localized disease activity of hydrocephalus and cauda equina syndrome. In the ventricular CSF, only the CEA level reflected the presence of hydrocephalus. We suggest using more specific biomarkers for the evaluation of ventricular CSF to monitor disease activity and treatment response.

• Animal Bioscience
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• v.36 no.7
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• pp.1044-1058
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• 2023

Objective: The objective of this study was to characterize physiochemical and nutrient profiles of feedstock and co-products from canola bio-oil processing that were impacted by source origin. The feedstocks and co-products (mash, pellet) were randomly collected from five different bio-oil processing plants with five different batches of samples in each bio-processing plant in Canada (CA) and China (CH). Methods: The detailed chemical composition, energy profile, total digestible nutrient (TDN), protein and carbohydrate subfractions, and their degradation and digestion (CNCPS6.5) were determined. Results: The results showed that TDN_1x was similar in meals between CA and CH. CH meals and feedstock had higher, truly digestible crude protein (tdCP) and neutral detergent fiber (tdNDF) than CA while CA had higher truly digestible non-fiber carbohydrate (tdNFC). The metabolizable energy (ME_3x), net energy (NE_Lp3x, NE_m3x, and NE_g3x) were similar in meals between CA and CH. No differences were observed in energy profile of seeds between CA and CH. The protein and carbohydrate subfractions of seeds within CH were similar. The results also showed that pelleting of meals affected protein sub-fractionation of CA meals, except rapidly degradable fractions (PB1), rumen degradable (RDPB1) and undegrdable PB1 (RUPB1), and intestinal digestible PB1 (DIGPB1). Canola meals were different in the soluble (PA2) and slowly degradable fractions (PB2) between CA and CH. The carbohydrate fractions of intermediately degradable fraction (CB2), slowly degradable fraction (CB3), and undegradable fraction (CC) were different among CH meals. CH presented higher soluble carbohydrate (CA4) and lower CB2, and CC than CA meals. Conclusion: The results indicated that although the seeds were similar within and between CA and CH, either oil-extraction process or meal pelleting seemed to have generated significantly different aspects in physiochemical and nutrient profiles in the meals. Nutritionists and producers need to regularly check nutritional value of meal mash and pellets for precision feeding.