• Journal of the Institute of Electronics Engineers of Korea CI
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• v.49 no.2
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• pp.123-133
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• 2012

This paper discuss about DNA watermarking using coding DNA sequence (CDS) for the authentication, the privacy protection, or the prevention of illegal copy and mutation of DNA sequence and propose a DNA watermarking scheme with the mutation robustness and the animo acid preservation. The proposed scheme selects a number of codons at the regular singularity in coding regions for the embedding target and embeds the watermark for watermarked codons and original codons to be transcribed to the same amino acids. DNA base sequence is the string of 4 characters, {A,G,C,T} ({A,G,C,U} in RNA). We design the codon coding table suitable to watermarking signal processing and transform the codon sequence to integer numerical sequence by this table and re-transform this sequence to floating numerical sequence of circular angle. A codon consists of a consecutive of three bases and 64 codons are transcribed to one from 20 amino acids. We substitute the angle of selected codon to one among the angle range with the same animo acid, which is determined by the watermark bit and the angle difference of adjacent codons. From in silico experiment by using HEXA and ANG sequences, we verified that the proposed scheme is more robust to silent and missense mutations than the conventional scheme and preserve the amino acids of the watermarked codons.

• The Korea Journal of Herbology
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• v.32 no.3
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• pp.19-27
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• 2017

Objectives : The aim of this study was to examine effect of anti-oxidant and anti-inflammation activity of the Kyeongok-go with various processing methods that was manufactured by heating mantle. Methods : Commercial Kyeongok-go (K0) was purchased and Kyeongok-go with ginseng (K1), Kyeongok-go with black ginseng (BK), ginseng fermentation Kyeongok-go (KF), black ginseng fermentation Kyeongok-go (BKF) were manufactured by heating mantle. To examine anti-oxidant effect, DPPH radical and production of NO and ROS in RAW 264.74 cell were used. Furthermore, to determined anti-inflammation effect, measured pro-inflammatory mRNA such as NOS-II, COX-2, $IL-1{\beta}$, IL-6, $TNF-{\alpha}$ in RAW 264.74 cell treated with K0, K1, KF, BK, and BKF. Result : K1 scavenged DPPH radical effectively than K0. The most DPPH radical scavenging activity was BKF. In the RAW 264.74 cells stimulated with LPS, NO and ROS production were measured. As a results, K1 was decreased NO, ROS production compared with K0, and BKF was reduced similarly to cyclosporine A (positive control). Expression of pro-inflammatory mRNA such as NOS-II, COX-2, $IL-1{\beta}$, IL-6 showed a significant decrease in BK or BKF. But, there was no significant in expression of $TNF-{\alpha}$ in all extract treatmetn groups. Conclusions : According to the above results, it is considered that Kyeongok-go with fermented black ginseng (BKF) manufactured by heating mantle is effective material that have anti-inflammation and anti-oxidant activities. Our finding indicate that BKF may be an effective agent for anti-inflammation through anti-oxidant effect.

• Molecules and Cells
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• v.27 no.5
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• pp.539-546
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• 2009

In Saccharomyces cerevisiae, ribosomal protein L7, one of the ~46 ribosomal proteins of the 60S subunit, is encoded by paralogous RPL7A and RPL7B genes. The amino acid sequence identity between RPl7a and RPl7b is 97 percent; they differ by only 5 amino acid residues. Interestingly, despite the high sequence homology, Rpl7b is detected in both the cytoplasm and the nucleolus, whereas Rpl7a is detected exclusively in the cytoplasm. A site-directed mutagenesis experiment revealed that the change in the amino acid sequence of Rpl7b does not influence its subcellular localization. In addition, introns of RPL7A and RPL7B did not affect the subcellular localization of Rpl7a and Rpl7b. Remarkably, Rpl7b was detected exclusively in the cytoplasm in rpl7a knockout mutant, and overexpression of Rpl7a resulted in its accumulation in the nucleolus, indicating that the subcellular localization of Rpl7a and Rpl7b is influenced by the intracellular level of Rpl7a. Rpl7b showed a wide range of localization patterns, from exclusively cytoplasmic to exclusively nucleolar, in knockout mutants for some rRNA-processing factors, nuclear pore proteins, and large ribosomal subunit assembly factors. Rpl7a, however, was detected exclusively in the cytoplasm in these mutants. Taken together, these results suggest that although Rpl7a and Rpl7b are paralogous and functionally replaceable with each other, their precise physiological roles may not be identical.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.81.2-82
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• 2003

Plants have evolved along with pathogens, and they have developed sophisticated defense systems against specific microorganisms to survive. G-protons are considered one of the upstream signaling components working as a key for the defense signal transduction pathway. For activation and inactivation of G-protein, GTP-biding proteins are involved. GTP -binding proteins are found in all organisms. Small GTP-binding proteins, having masses of 21 to 30kD, belong to a superfamily, often named the Ras supefamily because the founding members are encoded by human Ras genes initially discovered as cellular homologs of the viral ras oncogene. Members of this supefamily share several common structural features, including several guanine nucleotide binding domains and an effector binding domain. However, exhibiting a remarkable diversity in both structure and function. They are important molecular switches that cycle between the GDP-bound inactive form into the GTP-bound active form through GDP/GTP replacement. In addition, most GTP-binding proteins cycle between membrane-bound and cytosolic forms. such as the RAC family are cytosolic signal transduction proteins that often are involved in processing of extracellular stimuli. Plant RAC proteins are implicated in regulation of plant cell architecture secondary wall formation, meristem signaling, and defense against pathogens. But their molecular mechanisms and functions are not well known. We isolated a RacB homolog from rice to study its role of defense against pathogens. We introduced the constitutively active and the dominant negative forms of the GTP-hinging protein OsRacB into the wild type rice. The dominant negative foms are using two forms (full-sequence and specific RNA interference with RacB). Employing southern, and protein analysis, we examine to different things between the wild type and the transformed plant. And analyzing biolistic bombardment of onion epidermal cell with GFP-RacB fusion protein revealed association with the nucle.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.1
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• pp.17-22
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• 2004

A bacterial strain WJ-98 found to produce active extracellular keratinase was isolated from the soil of a poultry factory. It was identified as Paracoccus sp. based on its 16S rRNA sequence analysis, morphological and physiological characteristics. The optimal culture conditions for the production of keratinase by Paracoccus sp. WJ-98 were investigated. The optimal medium composition for keratinase production was determined to be 1.0% keratin, 0.05% urea and NaCl, 0.03% K$_2$HPO$_4$, 0.04% KH$_2$PO$_4$, and 0.01% MgCl$_2$$.$6H$_2$O. Optimal initial pH and temperature for the production of keratinase were 7.5 and 37$^{\circ}C$, respectively. The maximum keratinase production of 90 U/mL was reached after 84 h of cultivation under the optimal culturing conditions. The keratinase from Paracoccus sp. WJ-98 was partially purified from a culture broth by using ammonium sulfate precipitation, ion-exchange chromatography on DEAE-cellulose, followed by gel filtration chromatography on Sephadex G-75. Optimum pH and temperature for the enzyme reaction were pH 6.8 and 50$^{\circ}C$, respectively and the enzymes were stable in the pH range from 6.0 to 8.0 and below 50$^{\circ}C$. The enzyme activity was significantly inhibited by EDTA, Zn$\^$2+/ and Hg$\^$2+/. Inquiry into the characteristics of keratinase production from these bacteria may yield useful agricultural feed processing applications.

• Food Science and Biotechnology
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• v.16 no.3
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• pp.463-469
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• 2007

We examined the hepatoprotective effects of colored potato flakes on acetaminophen (AAP)-induced liver damage in rats. F344/DuCrj (8 week-old) rats were fed a cholesterol-free diet with 54.9486 g of ${\alpha}$-corn starch/100g diet and were orally treated with 25% colored flakes of Kitamurasaki (KM: light purple), Northern Ruby (NR: red), and Shadow Queen (SQ: medium purple) potatoes co-administered with AAP (0.5 g/100 g diet) for 4 weeks. The hepatic thiobarbituric acid-reactive substances (TBARS) values in the KM, NR, and SQ groups were significantly lower (p<0.05) than those in the control groups with and without AAP. Furthermore, the hepatic catalase, Mn-superoxide dismutase (SOD), and Cu/Zn-SOD mRNA levels in the KM, NR, and SQ groups were higher than those in the control groups with and without AAP. The present findings suggest that colored potato flakes are useful as a prophylactic agent against oxidative liver damage.

• Journal of Microbiology and Biotechnology
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• v.28 no.11
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• pp.1846-1849
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• 2018

Recent human gut microbiome studies have supported that the genus Bifidobacterium is one of the most beneficial bacteria for human intestinal health. To develop a new probiotic strain for functional food applications, fourteen fecal samples were collected from healthy Koreans and the strain BCBR-583 was newly selected and isolated from a 25-year-old Korean woman's fecal sample using the selective medium for Bifidobacterium. Subsequent fructose-6-phosphate phosphoketolase (F6PPK) test and 16S rRNA gene sequencing analysis of the strain BCBR-583 confirmed that it belongs to B. longum subsp. longum. The stress resistance tests showed that it has oxygen and heat tolerance activities (5- and 3.9-fold increase for 24 h at 60 and 120 rpm, respectively; $78.61{\pm}6.67%$ survival rate at $45^{\circ}C$ for 24 h). In addition, gut environment adaptation tests revealed that this strain may be well-adapted in the gut habitat, with gastric acid/bile salt resistance ($85.79{\pm}1.53%$, survival rate under 6 h treatments of gastric acid and bile salt) and mucin adhesion ($73.72{\pm}7.36%$). Furthermore, additional tests including cholesterol lowering assay showed that it can reduce $86.31{\pm}1.85%$ of cholesterol. Based on these results, B. longum BCBR-583 has various stress resistance for survival during food processing and environmental adaptation activities for dominant survival in the gut, suggesting that it could be a good candidate for fermented food applications as a new probiotic strain.

• The Korean Journal of Malacology
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• v.31 no.3
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• pp.243-247
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• 2015

A stand-alone BLAST server is available that provides a convenient and amenable platform for the analysis of molluscan sequence information especially the EST sequences generated by traditional sequencing methods. However, it is found that the server has limitations in the annotation of molluscan sequences generated using next-generation sequencing (NGS) platforms due to inconsistencies in molluscan sequence available at NCBI. We constructed a web-based interface for a new stand-alone BLAST, called PANM-DB (Protostome DB) for the analysis of molluscan NGS data. The PANM-DB includes the amino acid sequences from the protostome groups-Arthropoda, Nematoda, and Mollusca downloaded from GenBank with the NCBI taxonomy Browser. The sequences were translated into multi-FASTA format and stored in the database by using the formatdb program at NCBI. PANM-DB contains 6% of NCBInr database sequences (as of 24-06-2015), and for an input of 10,000 RNA-seq sequences the processing speed was 15 times faster by using PANM-DB when compared with NCBInr DB. It was also noted that PANM-DB show two times more significant hits with diverse annotation profiles as compared with Mollusks DB. Hence, the construction of PANM-DB is a significant step in the annotation of molluscan sequence information obtained from NGS platforms. The PANM-DB is freely downloadable from the web-based interface (Malacological Society of Korea, http://malacol.or/kr/blast) as compressed file system and can run on any compatible operating system.

• The Korean Journal of Malacology
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• v.29 no.2
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• pp.155-161
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• 2013

Cathepsins are lysosomal/cysteine proteases belong to papain family (C1 family) that is involved in intracellular protein degradation, antigen processing, hormone maturation, and immune responses. In this study, member of cathepsin family was identified from Manila clam (Mc-Cathepsin D) and investigated the immune response against brown ring disease (BRD) causing Vibrio tapetis challenge. The identified Mc-Cathepsin D gene encodes characteristic features typical for the cathepsin family including eukaryotic and viral aspartyl protease signature domain and two highly conserved active sites ($^{84}VVFDTGSSNLWV^{95}$ and $^{270}IADTGTSLLAG^{281}$). Moreover, MC-Cathepsin D shows higher identity values (-50-70%) and conserved amino acids with known cathepsin D members. Transcriptional results (by quantitative real-time RT-PCR) showed that Mc-Cathepsin D was expressed at higher levels in gills and hemocytes than mantle, adductor muscle, foot, and siphon. After the V. tapetis challenge under laboratory conditions, Mc-Cathepsin D mRNA was up-regulated in gills and hemocytes. Present study indicates that Mc-Cathepsin D is constitutively expressed in different tissues and potentially inducible when infecting BRD by V. tapetis. It is further suggesting that Mc-Cathepsin D may be involved in multiple role including immune response reactions against BRD.

• Molecules and Cells
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• v.40 no.9
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• pp.621-631
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• 2017

Vaccinia-related kinase 1 (VRK1) and VRK3 are members of the VRK family of serine/threonine kinases and are principally localized in the nucleus. Despite the crucial roles of VRK1/VRK3 in physiology and disease, the molecular and functional interactions of VRK1/VRK3 are poorly understood. Here, we identified over 200 unreported VRK1/VRK3-interacting candidate proteins by affinity purification and LC-MS/MS. The networks of VRK1 and VRK3 interactomes were found to be associated with important biological processes such as the cell cycle, DNA repair, chromatin assembly, and RNA processing. Interactions of interacting proteins with VRK1/VRK3 were confirmed by biochemical assays. We also found that phosphorylations of XRCC5 were regulated by both VRK1/VRK3, and that of CCNB1 was regulated by VRK3. In liver cancer cells and tissues, VRK1/VRK3 were highly upregulated and its depletion affected cell cycle progression in the different phases. VRK3 seemed to affect S phase progression and G2 or M phase entry and exit, whereas VRK1 affects G1/S transition in the liver cancer, which could be explained by different interacting candidate proteins. Thus, this study not only provides a resource for investigating the unidentified functions of VRK1/VRK3, but also an insight into the regulatory roles of VRK1/VRK3 in biological processes.