• Asian-Australasian Journal of Animal Sciences
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• v.26 no.8
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• KSBB Journal
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• v.30 no.6
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• pp.291-295
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• 2015

The limited productivity of natural shell matrix proteins has hampered the investigation of their biochemical properties and practical applications, although biominerals in nature obtained by organic-inorganic assemblies have attractive mechanical and biological properties. Here, we prepared a vector for the expression of a fusion protein of a shell matrix protein from Pinctada fucata (named as GRP_BA) with the GRGDSP residue. The fusion protein of BA-RGD was simply produced in E. coli and purified through sequential steps including the treatment with $CaCl_2$ and EDTA solution for cell membrane washing, mechanical cell disruption and the application of non-ionic surfactant of Triton X-100 for BA-RGD inclusion body washing. The production yield was approximately 60 mg/L, any other protein band was not observed in SDS-PAGE and it was estimated that above 97% endotoxin was removed compared to the endotoxin level of whole cell. This study showed this simple and easy purification approach could be applied to the purification of BA-RGD fusion protein. It is expected that the protein could be utilized for the preparation of biominerals in practical aspects.

• Korean Journal of Veterinary Research
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• v.43 no.1
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• pp.129-137
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• 2003

Porcine reproductive and respiratory syndrome (PRRS) is characterized by reproductive failures in sows and respiratory problems in piglets. The nucleocapsid(N) protein, encoded by the open reading frame 7 (ORF7) gene, is known to be the most abundant and antigenic protein in PRRS virus. Therefore, it was suggested that the N protein could be a suitable candidate for the detection of PRRS virus-specific antibodies and diagnosis of PRRS. In the present study, the ORF7 gene encoding the N protein was cloned and expressed as a fusion protein with the glutathione S-transferase (GST) in Escherichia coli. The resulting GST-N recombinant protein was used as an antigen for an indirect sandwich enzyme-linked immunosorbent assay (i-ELISA). Expressed GST-N recombinant protein was migrated at 41 kDa and reacted with ORF7-specific monoclonal antibody by Western blotting. In order to increase the specificity of the ELISA for the detection of PRRS virus-specific antibodes, an i-ELISA was developed using an anti-GST antibody as a capture antibody. The sensitivity and specificity of developed i-ELISA were 92% and 96%, respectively. Based on these results, it was suggested that the i-ELISA is a simple and rapid test for screening a large number of swine sera for the anti-PRRS virus antibodies.

• Journal of Life Science
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• v.21 no.8
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• pp.1067-1075
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• 2011

Coiled-coil domain-containing protein 98 (CCDC98) plays a role in G2/M DNA damage checkpoint pathways by recruiting breast cancer 1 (BRCA1)-A complex to the DNA-damaged sites. However, the molecular mechanism of CCDC98 on the DNA damage-induced G2/M checkpoint pathways is unclear. In this study, we identifed Wilms tumor 1-associating protein (WTAP) as a novel CCDC98-binding protein, using tandem affinity purification. We confirmed the association between CCDC98 and WTAP using in vivo and in vitro binding assays. We demonstrated that CCDC98 regulates cyclin B1 expression by affecting WTAP protein stability. Based on these results, we suggest that CCDC98 may act as a novel cell cycle regulator by regulating the expression level of cyclin B1.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.131-131
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• 2017

Though the Platycodon grandiflorum, has a broad range of pharmacologic properties, but the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two-dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}2-fold$) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, the frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). Taken together, the protein profile may provide insight clues for better understanding the characteristics of proteins and its metabolic activities in various explants of this essential medicinal plant P. grandiflorum.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.5
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• pp.712-718
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• 2004

This study was carried out to separate the calcium-binding protein derived from enzymatic hydrolysates of cheese whey protein. CWPs (cheese whey protein) heated for 10 min at $100^{\circ}C$ were hydrolyzed by trypsin, papain W-40, protease S, neutrase 1.5 and pepsin, and then properties of hydrolysates, separation of calcium-binding protein and analysis of calcium-binding ability were investigated. The DH (degree of hydrolysis) and NPN (non protein nitrogen) of heated-CWP hydrolysates by commercial enzymes were higher in trypsin than those of other commercial enzymes. In the result of SDS-PAGE (sodium dodecyl sulphate polyacrylamide gel electrophoresis), $\beta$-LG and $\alpha$-LA in trypsin hydrolysates were almost eliminated and the molecular weight of peptides derived from trypsin hydrolysates were smaller than 7 kDa. In the RP-HPLC (reverse phase HPLC) analysis, $\alpha$-LA was mostly eliminated, but $\beta$-LG was not affected by heat treatment and the RP-HPLC patterns of trypsin hydrolysates were similar to those of SDS-PAGE. In ion exchange chromatography, trypsin hydrolysates were shown to peak from 0.25 M NaCl and 0.5 M NaCl, and calcium-binding ability is associated with the large peak, which was eluted at a 0.25 M NaCl gradient concentration. Based on the results of this experiment, heated-CWP hydrolysates by trypsin were shown to have calcium-binding ability.

• 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.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.1
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• pp.97-106
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• 2015

Platycodon grandiflorum, commonly known as Doraji in Korea, has a wide range of pharmacologic properties, such as reducing adiposity and hyperlipidemia, and antiatherosclerotic effects. However, the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}$ 2-fold) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). In that way, the exclusive protein profile may provide insight clues for better understanding the characteristics of proteins and metabolic activity in various explants of the economically important medicinal plant Platycodon grandiflorum.

• Genomics & Informatics
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• v.19 no.4
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• pp.46.1-46.11
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• 2021

Moringa oleifera is nowadays raising as the most preferred medicinal plant, as every part of the moringa plant has potential bioactive compounds which can be used as herbal medicines. Some bioactive compounds of M. oleifera possess potential anti-cancer properties which interact with the apoptosis protein p53 in cancer cell lines of oral squamous cell carcinoma. This research work focuses on the interaction among the selected bioactive compounds derived from M. oleifera with targeted apoptosis protein p53 from the apoptosis pathway to check whether the bioactive compound will induce apoptosis after the mutation in p53. To check the toxicity and drug-likeness of the selected bioactive compound derived from M. oleifera based on Lipinski's Rule of Five. Detailed analysis of the 3D structure of apoptosis protein p53. To analyze protein's active site by CASTp 3.0 server. Molecular docking and binding affinity were analyzed between protein p53 with selected bioactive compounds in order to find the most potential inhibitor against the target. This study shows the docking between the potential bioactive compounds with targeted apoptosis protein p53. Quercetin was the most potential bioactive compound whereas kaempferol shows poor affinity towards the targeted p53 protein in the apoptosis pathway. Thus, the objective of this research can provide an insight prediction towards M. oleifera derived bioactive compounds and target apoptosis protein p53 in the structural analysis for compound isolation and in-vivo experiments on the cancer cell line.

• Applied Biological Chemistry
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• v.13 no.1
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• pp.65-72
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• 1970

Two peptides (Im pr-M, Im ch-M) derived from Im ${\lambda}-type$ of Bence Jones Protein and one peptide (Ikch-M) from Ik were separated and purified using the Dowex $50{\times}2$ column $(1{\times}20\;cm)$ and Dowex $1{\times}2(0.9{\times}50\;cm)$. The buffer solution was composed of 1% pyridine and IM formic acid in Dowex $1{\times}2$ column. The blocked N-terminal was examined with ninhydrin reaction before and after alkaline hydrolysis, which was fractionated by Dowex $1{\times}2$ column. Pyrro-glutamic acid in N-terminal residue was identified by comparing with the authentic pyrro-glutamic acid through a high voltage electrophoresis (pH 3.5, 3000 V.) after the peptide Im pr-M (PCA. Ser) was cleavaged at the position of serine with cone. (12 N) HCl and the pyrro-glutamic acid was converted to glutamic acid by treating it with N-NaOH for 116 hours at $27^{\circ}C$. The substractive method was applied to find out the sequence of peptides and carboxypeptidase A was employed to release C-terminal residue from the peptide. In present study PCA. Ser in Im Pr-M was isolated from the pronase digested ${\lambda}$-type Bence Jones protein. The yield of the Im Pr-M was 79.6 percent of its theoretical value, based on the molecular weight of Bence Jones Protein. Im ch-M (PCA. Ser Val. Leu) was isolated from the chymotrypsin digested ${\lambda}$-type Bence Jones Protein. The yield of the Im ch-M was 72.2 percent. based on the molecular weight of Bence Jones Protein. Ik ch-M (PCA. Ser. Ala. Leu) was isolated from the chymotrypsin digested ${\lambda}$-type Bence Jones Protein and its yield was 42% based on the molecular weight of Bence Jones Protein.