• Genomics & Informatics
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• v.7 no.4
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• pp.217-219
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• 2009

The primary clue for locating protein-coding regions is the open reading frame and the determination of ORFs (Open Reading Frames) is the first step toward the gene prediction, especially for prokaryotes. In this respect, we have developed a web-based ORF search tool called ORF Miner. The ORF Miner is a graphical analysis utility which determines all possible open reading frames of a selectable minimum size in an input sequence. This tool identifies all open reading frames using alternative genetic codes as well as the standard one and reports a list of ORFs with corresponding deduced amino acid sequences. The ORF Miner can be employed for sequence annotation and give a crucial clue to determination of actual protein-coding regions.

• Korean Journal of Environmental Biology
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• v.27 no.1
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• pp.95-99
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• 2009

Transcriptomic changes in the brain of Limanda yokohamae were investigated to understand the environmental condition of Masan Bay, Korea. Differentially expressed genes (DEGs) in the brain of the flat fish from Masan Bay were identified by comparing those from the reference site Gangneung using annealing control primers-based polymerase chain reaction. The results demonstrated that two different kinds of the cytoplasmic ribosomal proteins, 40 s ribosomal protein S27a and ribosomal protein L6, were identified by the BLAST searching followed by sequence analysis. These findings suggest that environmental status of Masan Bay could hinder protein synthesis that is required for maintaining brain functions and thus cause the dysfunction of fish physiology.

• Food Science and Industry
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• v.54 no.3
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• pp.171-183
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• 2021

Tofu has been consumed as source of protein in Asia for hundreds of years and it was first known in US and Europe by Asian immigrants during 1900s. Lately it is being spotlighted for excellent plant-based protein that has nutritional value. Tofu has long been the most widely used ingredients in Asia and it has been developed into various forms such as tofu, yuba, fried tofu, tofu sheet, fermented tofu and more according to food culture. With development of equipment, coagulant, packaging and pasteurization, now we can have advanced flavor, productivity and distribution of tofu. Tofu has been brought to customer's attention, people who prefer more health oriented, sustainable and eco-friendly food during COVID-19 pandemic season. Furthermore, this global trend is expected to be continued. In response to the trend we need more study on new texture of tofu, substitution of meat, dairy, and various commercialization of HMR in future.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.103-108
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• 2006

Computational prediction of protein-ligand binding has been widely used as a tool to discover lead compounds fur new drugs. Prediction accuracy is determined in part by the scoring function used in docking calculations. Diverse scoring functions are available, and these can be classified into force-field based, empirical, and knowledge-based functions depending upon the basic assumptions made in development. Among these, force-field based functions consider physical interactions the most in detail. However, the force-field based functions have the drawback of not including the entropic effect while considering only the energy contribution such as dispersion or electrostatic forces. In this article, a method to take into account of the entropic effect using the colony energy is suggested when force-field based scoring functions is used by extracting conformational information obtained from the pre-existing docking program. An improved result for decoy discrimination is illustrated when the method is applied to the DOCK scoring function, and this implies that more accurate docking calculation is possible.

• Korean Journal of Clinical Laboratory Science
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• v.51 no.1
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• pp.78-85
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• 2019

Membrane proteins are involved in many common diseases, including heart disease and cancer. In various disease states, such as cancer, abnormal signaling pathways that are related to the membrane proteins cause the cells to divide out of control and the expression of membrane proteins can be altered. Membrane proteins have the hydrophobic environment of a lipid bilayer, which makes an analysis of the membrane proteins notoriously difficult. Therefore, this study evaluated the efficacy of two different methods for optimal membrane protein extraction. High-speed centrifuge and reagent-based method with a -/+ filter aided sample preparation (FASP) were compared. As a result, the high-speed centrifuge method is quite effective in analyzing the mitochondrial inner membranes, while the reagent-based method is useful for endoplasmic reticulum membrane analysis. In addition, the function of the membrane proteins extracted from the two methods were analyzed using GeneGo software. GO processes showed that the endoplasmic reticulum-related responses had higher significance in the reagent-based method. An analysis of the process networks showed that one cluster in the high-speed centrifuge method and four clusters in the reagent-based method were visualized. In conclusion, the two methods are useful for the analysis of different subcellular membrane proteins, and are expected to assist in selecting the membrane protein extraction method by considering the target subcellular membrane proteins for study.

• Animal Bioscience
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• v.36 no.8
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• pp.1228-1240
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• 2023

Objective: This experiment was conducted to evaluate the effects of different levels of dietary crude protein (CP) on growth performance, blood profiles, diarrhea incidence, nutrient digestibility, and odor emission in weaning pigs. Methods: A total of 240 weaning ([Yorkshire×Landrace]×Duroc) pigs (8.25±0.050 kg body weight [BW]) were assigned to six treatments based on sex and initial BW, with five replicates of eight pigs per pen in a randomized complete block design. Experimental diets with different crude protein levels for early and late weaning phases were as follows: i) CP16, corn-soybean-based diet containing 16%/15% CP; ii) CP17, corn-soybean-based diet containing 17%/16% CP; iii) CP18, corn-soybean-based diet containing 18%/17% CP; iv) CP19, corn-soybean-based diet containing 19%/18% CP; v) CP20, corn-soybean-based diet containing 20%/19% CP; and vi) CP21, corn-soybean-based diet containing 21%/20% CP. Results: In the early weaning period, average daily feed intake increased when the dietary CP level decreased (linear, p<0.05). During the entire experimental period, average daily gain and the gain to feed ratio decreased when the dietary CP level increased (linear, p<0.01). Additionally, a decrease in dietary CP level resulted in a linear increase in final BW (linear, p<0.05). In the early and late weaning periods, blood urea nitrogen (BUN) decreased when the dietary CP level decreased (linear, p<0.01). There were no significant differences in creatinine, glucose, total protein, triglyceride or insulin-like factor-1 levels over the experimental period. The concentrations of immunoglobulin A (IgA) and IgG were not significantly affected by dietary CP levels during the experimental period. In the early weaning period, fecal and urine N decreased when the dietary CP level decreased (linear, p<0.01). No differences in nutrient digestibility among the treatments during the early weaning period were found. Throughout the whole experimental period, when the dietary CP level decreased in the weaning pig diet, the diarrhea incidence decreased linearly (linear, p<0.01). Throughout the whole experimental period, when the dietary CP level decreased in the weaning pig diet, ammonia, amines and hydrogen sulfide decreased linearly (linear, p<0.01). Conclusion: Reducing dietary CP could decrease diarrhea incidence, the concentration of BUN in serum and odor emission in manure. Furthermore, it could improve N excretion in feces and urine and growth performance in weaning pigs.

• BMB Reports
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• v.39 no.1
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• pp.55-60
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• 2006

We describe a phage display strategy, based on the differential resistance of proteins to denaturant-induced unfolding, that can be used to select protein variants with improved conformational stability. To test the efficiency of this strategy, wild-type and two stable variants of ${\alpha}_1$-antitrypsin (${\alpha}_1AT$) were fused to the gene III protein of M13 phage. These phages were incubated in unfolding solution containing denaturant (urea or guanidinium chloride), and then subjected to an unfavorable refolding procedure (dialysis at $37^{\circ}C$). Once the ${\alpha}_1AT$ moiety of the fusion protein had unfolded in the unfolding solution, in which the denaturant concentration was higher than the unfolding transition midpoint ($C_m$) of the ${\alpha}_1AT$ variant, around 20% of the phage retained binding affinity to anti-${\alpha}_1AT$ antibody due to a low refolding efficiency. Moreover, this affinity reduced to less than 5% when 10 mg/mL skimmed milk (a misfolding-promoting additive) was included during the unfolding/refolding procedure. In contrast, most binding affinity (>95%) remained if the ${\alpha}_1AT$ variant was stable enough to resist unfolding. Because this selection procedure does not affect the infectivity of M13, the method is expected to be generally applicable to the high-throughput screening of stable protein variants, when activity-based screening is not possible.

• Journal of Microbiology and Biotechnology
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• v.23 no.8
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• pp.1116-1122
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• 2013

Cell line development is the most critical and also the most time-consuming step in the production of recombinant therapeutic proteins. In this regard, a variety of vector and cell engineering strategies have been developed for generating high-producing mammalian cells; however, the cell line engineering approach seems to show various results on different recombinant protein producer cells. In order to improve the secretory capacity of a recombinant tissue plasminogen activator (t-PA)-producing Chinese hamster ovary (CHO) cell line, we developed cell line engineering approaches based on the ceramide transfer protein (CERT) and X-box binding protein 1 (XBP1) genes. For this purpose, CERT S132A, a mutant form of CERT that is resistant to phosphorylation, and XBP1s were overexpressed in a recombinant t-PA-producing CHO cell line. Overexpression of CERT S132A increased the specific productivity of t-PA-producing CHO cells up to 35%. In contrast, the heterologous expression of XBP1s did not affect the t-PA expression rate. Our results suggest that CERT-S132A-based secretion engineering could be an effective strategy for enhancing recombinant t-PA production in CHO cells.

• Nutrition Research and Practice
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• v.9 no.4
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• pp.343-349
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• 2015

BACKGROUND/OBJECTIVES: Fermentation of dietary fiber results in production of various short chain fatty acids in the colon. In particular, butyrate is reported to regulate the physical and functional integrity of the normal colonic mucosa by altering mucin gene expression or the number of goblet cells. The objective of this study was to investigate whether butyrate modulates mucin secretion in LS174T human colorectal cells, thereby influencing the adhesion of probiotics such as Lactobacillus and Bifidobacterium strains and subsequently inhibiting pathogenic bacteria such as E. coli. In addition, possible signaling pathways involved in mucin gene regulation induced by butyrate treatment were also investigated. MATERIALS/METHODS: Mucin protein content assay and periodic acid-Schiff (PAS) staining were performed in LS174T cells treated with butyrate at various concentrations. Effects of butyrate on the ability of probiotics to adhere to LS174T cells and their competition with E. coli strains were examined. Real time polymerase chain reaction for mucin gene expression and Taqman array 96-well fast plate-based pathway analysis were performed on butyrate-treated LS174T cells. RESULTS: Treatment with butyrate resulted in a dose-dependent increase in mucin protein contents in LS174T cells with peak effects at 6 or 9 mM, which was further confirmed by PAS staining. Increase in mucin protein contents resulted in elevated adherence of probiotics, which subsequently reduced the adherent ability of E. coli. Treatment with butyrate also increased transcriptional levels of MUC3, MUC4, and MUC12, which was accompanied by higher gene expressions of signaling kinases and transcription factors involved in mitogen-activated protein kinase (MAPK) signaling pathways. CONCLUSIONS: Based on our results, butyrate is an effective regulator of modulation of mucin protein production at the transcriptional and translational levels, resulting in changes in the adherence of gut microflora. Butyrate potentially stimulates the MAPK signaling pathway in intestinal cells, which is positively correlated with gut defense.

• Journal of Ginseng Research
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• v.44 no.5
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• pp.680-689
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• 2020

Background: Peptides have diverse and important physiological roles in plants and are ideal markers for species identification. It is unclear whether there are specific peptides in Panax quinquefolius L. (PQ). The aims of this study were to identify Quinetides, a series of diverse posttranslational modified native peptides of the ribonuclease-like storage protein (ginseng major protein), from PQ to explore novel peptide markers and develop a new method to distinguish PQ from Panax ginseng. Methods: We used different fragmentation modes in the LTQ Orbitrap analysis to identify the enriched Quinetide targets of PQ, and we discovered Quinetide markers of PQ and P. ginseng using ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry analysis. These "peptide markers" were validated by simultaneously monitoring Rf and F11 as standard ginsenosides. Results: We discovered 100 Quinetides of PQ with various post-translational modifications (PTMs), including a series of glycopeptides, all of which originated from the protein ginseng major protein. We effectively distinguished PQ from P. ginseng using new "peptide markers." Four unique peptides (Quinetides TP6 and TP7 as markers of PQ and Quinetides TP8 and TP9 as markers of P. ginseng) and their associated glycosylation products were discovered in PQ and P. ginseng. Conclusion: We provide specific information on PQ peptides and propose the clinical application of peptide markers to distinguish PQ from P. ginseng.