• KSBB Journal
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• v.19 no.1
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• pp.42-49
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• 2004

A gene coding for epoxide hydrolase (EH) of Aspergillus niger LK, a fungus possessing the enantioselective hydrolysis activity for racemic epoxides, was characterized by phylogenetic analysis. The deduced protein of A. niger LK epoxide hydrolase shares significant sequence similarity with several bacterial EHs and mammalian microsomal EHs (mEH) and belongs to the a/${\beta}$ hydrolase fold family. EH from A. niger LK had 90.6% identity with 3D crystal structure of lqo7 in Protein Data Bank. Sequence comparison with other source EHs suggested that Asp$\^$l92/, Asp$\^$374/ and His$\^$374/ constituted the catalytic triad. Based on the multiple sequence comparison of the functional and structural domain sequence, the phylogenetic tree between relevant epoxide hydrolases from various species were reconstructed by using Neighbor-Joining method. Genetic distances were so far as 1.841-2.682 but characteristic oxyanion hole and catalytic triad were highly conserved, which means they have diverged from a common ancestor.

• BMB Reports
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• v.41 no.6
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• pp.448-454
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• 2008

Two full-length cDNAs, PutPMP3-1 and PutPMP3-2, encoding PMP3 family proteins were isolated from Puccinellia tenuiflora, a monocotyledonous halophyte. Expression of both genes was induced by low temperature, salt stress, dehydration, ABA, and $NaHCO_3$. Transcripts of PutPMP3-2 were more strongly induced by these stresses relative to those of PutPMP3-1, particularly under low temperature and dehydration conditions. Expression of PutPMP3-1 and PutPMP3-2 in yeast mutants lacking the PMP3 gene can functionally complement the membrane hyper-polarization and salt sensitivity phenotypes resulting from PMP3 deletion. To compare the functions of PutPMP3-1 and PutPMP3-2, the orthologous genes in rice (OsLti6a and OsLti6b) were isolated. Both OsLti6a and OsLti6b could functionally complement the loss of PMP3 in yeast. PutPMP3-2 and OsLti6a were more effective in reversing membrane hyperpolarization than PutPMP3-1 and OsLti6b. However, the four yeast transformants each showed similar levels of salt tolerance. These results imply that these PMP3 family members don't function identically under different stress tolerance conditions.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.48 no.6
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• pp.913-919
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• 2015

In vertebrates, the vitamin D receptor (VDR), a member of the nuclear receptor superfamily, binds the biologically active ligand $1{\alpha},25-(OH)_2$-vitamin $D_3$ (1,25 $D_3$). Nearly all vertebrates, including Agnatha, possess a VDR with high ligand selectivity for 1,25 $D_3$ and related metabolites. Although a putative ancestral VDR gene is present in the genome of the chordate invertebrate Ciona intestinalis, the functional characteristics of marine invertebrate VDR are still obscure. To elucidate the ascidian Halocynthia roretzi VDR (HrVDR), we cloned full-length HrVDR cDNA and investigated the transcriptional activity of HrVDR in HEK293 cells. HrVDR consists of 1,680 nucleotides (559 amino acids [aa]), including a short N-terminal region (A/B domain; 26 aa), DNA-binding domain (C domain; 72 aa), hinge region (D domain; 272 aa), and C-terminal ligand-binding domain (E domain; 161 aa). The amino acid sequence identity of HrVDR was greatest to that of C. intestinalis VDR (56%). In the luciferase reporter assays, the transcriptional activity of HrVDR was not significantly increased by 1,25 $D_3$, whereas the farnesoid X receptor agonist GW4064 increased the transactivation of HrVDR. These results suggest the presence of a novel ligand for and a distinct ligand-binding domain in ascidian VDR.

• BMB Reports
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• v.39 no.6
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• pp.749-758
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• 2006

The cytosolic members of the HSP70 family of proteins play key roles in the molecular chaperone machinery of the cell. In the study we cloned and sequenced the full-length cDNA of Delia antiqua HSP70 gene, which is 2461 bp long and encodes 643 a.a. with a calculated molecular mass of 70,787 Da. We investigated gene copies of cytosolic HSP70 members of 4 insect species with complete genome available, and found that they are quite variable with species. In order to characterize this protein we carried out an alignment and a phylogenetic analysis with 41 complete protein sequences from insects. The analysis divided the cytosolic members of the family into two classes, HSP70 and HSC70, distinguishable on the basis of 15 residues. HSP70 class members were slightly shorter in length and smaller in molecular mass relative to the HSC70 class members, and the conservative and functional regions in these sequences were documented. Mainly, we investigated the expression of Delia antiqua HSP70 gene, in response to diapauses and thermal stresses. Both summer and winter diapauses elevated HSP70 transcript levels. Cold-stress led to increased HSP70 expression levels in summer- and winter-diapausing pupae, but heat-stress elevated the levels only in the winter-diapausing pupae. In all cases, the expression levels, after being elevated, gradually decreased with time. HSP70 expression was low in non-diapausing pupae but was up-regulated following cold- and heat-stresses. Heat-stress gradually increased the mRNA level with time whereas cold-stress gradually decreased levels after an initial increase.

• Polymer(Korea)
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• v.28 no.2
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• pp.177-184
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• 2004

Polymer-clay nanocomposite containing the low amounts of clay shows improved physical, mechanical properties. In this study, allyl ester prepolymer was synthesised by reactions of the diallyl terephthalate monomers and the 1,3-butanediol monomers. Nanocomposites of allyl ester prepolymer and the two kinds of the organically layered silicate were prepared by using the intercalation method as well as the in-situ polymerization method using. By varying the amount of clay content, curing conditions, and feeding conditions. the nanocomposite was studied using X-ray diffraction. From XRD results, allyl ester-Cloisite 30 B nanocomposite made by the in-situ polymerization method shows better exfoliation behavior compared with the intercalation method. It can be said that the transesterification reaction between functional groups (-OH) of intercalant and monomers results in the increased gallery distance. Also mechanical and thermal properties indicate that the dispersity of clay is an important factor for improving physical properties of the nanocomposite.

• Restorative Dentistry and Endodontics
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• v.29 no.4
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• pp.399-408
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• 2004

Odontoblasts are responsible for the formation and maintenance of dentin. They are known to synthesize unique gene products including dentin sialophosphoprotein (DSPP). Another unique genes of the cells remain unclear. OD314 was isolated from the odontoblasts/pulp cells of rats and partially characterized as an odontoblast-enriched gene (Dey et al., 2001). This study aimed to elucidate the biological function of OD314, relating to odontoblast differentiation and dentinogenesis. After determining the open reading frame (ORP) of OD314 by transient transfection analysis using green fluorescent protein (GPP) expression vector, mRNA in-situ hybridization, immunohistochemistry, reverse transcription-polymerase chain reaction (RT-PCR) and western analysis were performed. The results were as follows: 1. In in-situ hybridization, OD314 mRNAs were expressed in odontoblasts of developing coronal and root pulp. 2. OD314 was a novel protein encoding 154 amino acids, and the protein was mainly expressed in cytoplasm by transient transfection analysis. 3. Mineralized nodules were associated with multilayer cell nodules in the culture of human dental pulp cells and first detected from day 21 using alizarin-red S staining. 4. In RT-PCR analysis, OD314, osteocalcin (OC) and DSPP strongly expressed throughout 28 days of culture. Whereas, osteonectin (ON) mRNA expression stayed low up to day 14, and then gradually decreased from day 21. 5. Western blots showed an approximately 17 kDa band. OD314 protein was expressed from the start of culture and then increased greatly from day 21. In conclusion, OD314 is considered as an odontoblast-enriched gene and may play important roles in odontoblast differentiation and dentin mineralization.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.48 no.1
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• pp.26-35
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• 2015

This study compared the meat quality of sea rainbow trout Oncorhynchus mykiss frame muscle (S-FR-TY) and fillet (S-FI-TY) with the frame muscle of freshwater rainbow trout (F-FR). There was a difference of < 1% in the proximate composition of S-FR-TY vs. S-FI-TY, and of S-FR-TY vs. F-FR. The Hunter a value of F-FR-TY was lower compared with that of F-FR cultured in Jecheon (F-FR-JC), but higher than that of F-FR cultured in Pyeongtaek (F-FR-PT). However, no difference in the Hunter a value of S-FR-TY compared with any other F-FR was observed. The odor intensity of S-FR-TY was lower compared with that of F-FR, while the taste of S-FR-TY was milder than that of S-FI-TY, but stronger than that of F-FR. Although its total amino acid content was lower, the essential amino acid content of S-FR-TY was higher compared with S-FI-TY; the potassium content of S-FR-TY was also significantly greater. S-FR-TY contained high levels of nutritional and functional components, such as anserine, lysine, threonine, and eicosapentaenoic and docosahexaenoic acid. These results suggest that S-FR-TY could be used as a resource of canned food or fish jerky for children.

• Journal of Microbiology and Biotechnology
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• v.25 no.1
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• pp.18-25
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• 2015

To understand the metabolism of flavonoid rhamnoglycosides by human intestinal microbiota, we measured the metabolic activity of rutin and poncirin (distributed in many functional foods and herbal medicine) by 100 human stool specimens. The average α-L-rhamnosidase activities on the p-nitrophenyl-α-L-rhamnopyranoside, rutin, and poncirin subtrates were 0.10 ± 0.07, 0.25 ± 0.08, and 0.15 ± 0.09 pmol/min/mg, respectively. To investigate the enzymatic properties, α-L-rhamnosidase-producing bacteria were isolated from the specimens, and the α-L-rhamnosidase gene was cloned from a selected organism, Bifidobacterium dentium, and expressed in E. coli. The cloned α-L-rhamnosidase gene contained a 2,673 bp sequcence encoding 890 amino acid residues. The cloned gene was expressed using the pET 26b(+) vector in E. coli BL21, and the expressed enzyme was purified using Ni²⁺-NTA and Q-HP column chromatography. The specific activity of the purified α-L-rhamnosidase was 23.3 µmol/min/mg. Of the tested natural product constituents, the cloned α-L-rhamnosidase hydrolyzed rutin most potently, followed by poncirin, naringin, and ginsenoside Re. However, it was unable to hydrolyze quercitrin. This is the first report describing the cloning, expression, and characterization of α-L-rhamnosidase, a flavonoid rhamnoglycosidemetabolizing enzyme, from bifidobacteria. Based on these findings, the α-L-rhamnosidase of intestinal bacteria such as B. dentium seem to be more effective in hydrolyzing (1 →6) bonds than (1 →2) bonds of rhamnoglycosides, and may play an important role in the metabolism and pharmacological effect of rhamnoglycosides.

• Journal of Microbiology and Biotechnology
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• v.28 no.7
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• pp.1185-1198
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• 2018

The nucleosomal organization of chromatin using histone proteins is a fundamental and ubiquitous feature of eukaryotic nuclei, with the major exception of dinoflagellates. Although a number of recent genomic and transcriptomic analyses have detected numerous histone genes in dinoflagellates, little is known about their expression. Here in, we aimed to investigate the expression pattern of histone genes under nutritional stress, and an attempt was made to detect histone expression at the protein level in Alexandrium pacificum. The presence of histones at the mRNA level was confirmed in this study by the amplification, cloning, and sequencing of 10 different genes. Relative expression profiling of these genes under different growth conditions was determined with real-time PCR and revealed considerable levels of histone transcription in nutritionally stressed cells. We were unable to detect the expression of histones at the protein level even after immunodetection and analysis using mass spectrometry, although a histone-like protein was detected as a major nuclear component. A. pacificum expresses multiple variants of histone, and protein sequences revealed both conservation and divergence with respect to other eukaryotes. We concluded that A. pacificum maintained an active transcription of histone genes within the cell, and enhanced expression of histone genes in nutritional stress strongly suggest that histones have functional significance in dinoflagellates, although expression at the protein level was below our current detection limits, which suggests a limited role of histones in DNA packaging. Finally, the plausible regulation of histone expression at the gene and protein levels in A. pacificum is discussed.

• Journal of Microbiology and Biotechnology
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• v.30 no.5
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• pp.726-732
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• 2020

Indonesian kefir grains are potential sources of lactic acid bacteria (LAB) that may act as probiotics with specific functional properties. In this study we explored the potential of the probiotic and cholesterol-lowering effect of LAB isolated from Indonesian kefir grains obtained from Bogor, Bandung, Jakarta, and Yogyakarta. The results revealed that 10 isolates showed considerable survivability at low pH and bile salt with total cell reduction of ~3 log colony-forming units per milliliter after exposure to pH 2.5 and 0.5% (w/v) bile salt for 1 and 3 h, respectively. All strains exhibited strong antimicrobial activities against pathogenic bacteria and were sensitive to a wide spectrum of antibiotics but exhibited weak bile salt hydrolase activity. Identification based on 16S RNA suggested that nine isolates were Lactobacillus kefiri and one was Lactobacillus rhamnosus. The ability of the isolates to reduce cholesterol from the media varied, ranging from 22.08% to 68.75% with the highest reduction shown by L. kefiri JK17. The ability to remove cholesterol from the media decreased greatly in resting and dead cells, ranging from 14.58% to 22.08% in resting cells and from 7.89% to 18.17% in dead cells. It can be concluded that Indonesian kefir grains contain LAB potentially acting as probiotics capable of reducing cholesterol. The cholesterol-lowering effect especially occurs when the cells are metabolically active.