• The Korean Journal of Malacology
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• v.28 no.4
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• pp.377-384
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• 2012

The importance of biological resources has been gradually increasing, and mollusks have been utilized as main fishery resources in terrestrial ecosystems. But little is known about genomic and transcriptional analysis in mollusks. This is the first report on the transcriptomic profile of Meretrix lusoria. In this study, we constructed cDNA library and determined 542 of distinct EST sequences composed of 284 singletons and 95 contigs. At first, we identified 180 of EST sequences that have significant hits on protein sequences of the exclusive Mollusks database through BLASTX program and 343 of EST sequences that have significant hits on NCBI NR database. We also found that 211 of putative sequences through local BLAST (blastx, E < e-10) search against KOG database were classified into 16 functional categories. Some kinds of immune response related genes encoding allograft inflammatory factor 1 (AIF-1), B-cell translocation gene 1 (BTG1), C-type lectin A, thioester-containing protein and 26S proteasome regulatory complex were identified. To determine phylogenetic relationship, we identified partial sequences of four genes (COX1, COX2, 12S rRNA and NADH dehydrogenase) that significantly matched with the mitochondrial genomes of 3 species-Ml (Meretrix lusoria), Mp (Meretrix petechialis) and Mm (Meretrix meretrix). As a result, we found that there was a little bit of a difference between sequences of Korean isolates and other known isolates. This study will be useful to develop breeding technology and might also be helpful to establish a classification system.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1555-1561
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• 2016

Shank skin color of Korean native chicken (KNC) shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [$L^*$], redness [$a^*$], and yellowness [$b^*$]) were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL) analyses. We detected a major QTL that affects $b^*$ value (logarithm of odds [LOD] = 47.5, $p=1.60{\times}10^{-49}$) on GGA24 (GGA for Gallus gallus). At the same location, we also detected a QTL that influences $a^*$ value (LOD = 14.2, $p=6.14{\times}10^{-16}$). Additionally, beta-carotene dioxygenase 2 (BCDO2), the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA) and quantitative transmission disequilibrium test (QTDT). Significant associations were detected between BCDO2 g.9367 A>C and $a^*$ ($P_{MGA}=1.69{\times}10^{-28}$; $P_{QTDT}=2.40{\times}10^{-25}$). The strongest associations were between BCDO2 g.9367 A>C and $b^*$ ($P_{MGA}=3.56{\times}10^{-66}$; $P_{QTDT}=1.68{\times}10^{-65}$). However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.1
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• pp.126-133
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• 2016

A gene from Actinomyces sp. Korean native goat (KNG) 40 that encodes an endo-${\beta}$-1,4-glucanase, EG1, was cloned and expressed in Escherichia coli (E. coli) $DH5{\alpha}$. Recombinant plasmid DNA from a positive clone with a 3.2 kb insert hydrolyzing carboxyl methyl-cellulose (CMC) was designated as pDS3. The entire nucleotide sequence was determined, and an open-reading frame (ORF) was deduced. The ORF encodes a polypeptide of 684 amino acids. The recombinant EG1 produced in E. coli $DH5{\alpha}$ harboring pDS3 was purified in one step using affinity chromatography on crystalline cellulose and characterized. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis/zymogram analysis of the purified enzyme revealed two protein bands of 57.1 and 54.1 kDa. The amino terminal sequences of these two bands matched those of the deduced ones, starting from residue 166 and 208, respectively. Putative signal sequences, a Shine.Dalgarno-type ribosomal binding site, and promoter sequences related to the consensus sequences were deduced. EG1 has a typical tripartite structure of cellulase, a catalytic domain, a serine-rich linker region, and a cellulose-binding domain. The optimal temperature for the activity of the purified enzyme was $55^{\circ}C$, but it retained over 90% of maximum activity in a broad temperature range ($40^{\circ}C$ to $60^{\circ}C$). The optimal pH for the enzyme activity was 6.0. Kinetic parameters, $K_m$ and $V_{max}$ of rEG1 were 0.39% CMC and 143 U/mg, respectively.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.8
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• pp.3447-3450
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• 2015

Objective: To explore the sensitivity of gastric cancer cells to chemotherapy drugs in elderly patients and its correlation with cyclooxygenase-2 (COX-2) expression in cancer tissue. Materials and Methods: Forty-three elderly patients with gastric cancer (observation group) and 31 young patients with gastrointestinal tumors (control group) who were all diagnosed by pathology and underwent surgery in the 89th Hospital of Chinese People's Liberation Army were selected. Drug sensitivity testing of tumor cells in primary culture was carried out in both groups using a methyl thiazolyl tetrazolium (MTT) method, and the expression of COX-2 and the factors related to multi-drug resistance (MDR) in cancer tissue were assessed by immunohistochemistry. Results: The inhibition rates (IR) of vincristine (VCR), 5-fluorouracil (5-FU), oxaliplatin (L-OHP), mitomycin (MMC) and epirubicin (eADM) on tumor cells in the observation group were dramatically lower than in the control group, with statistical significance (P<0.05 or P<0.01). The positive rates of COX-2, glutathione s-transferase-${\pi}$ (GST-${\pi}$) and P glycoprotein (P-gp) expression in cancer tissue in the observation group were all higher than in control group (P<0.05), while that of DNA topoisomerase $II{\alpha}$ ($TopoII{\alpha}$) expression lower than in the control group (P<0.01). In the observation group, COX-2 expression in cancer tissue had a significantly-positive correlation with GST-${\pi}$ and P-gp (r=0.855, P=0.000; r=0.240, P=0.026), but a negative correlation with $TopoII{\alpha}$ (r=-0.328, P=0.002). In the control group, COX-2 expression in cancer tissue was only correlated with P-gp positively (r=0.320, P=0.011). Bivariate correlation analysis displayed that COX-2 expression in cancer tissue in the observation group had a significantly-negative correlation with the IRs of 5-FU, L-OHP, paclitaxel (PTX) and eADM in tumor cells (r=-0.723, P=0.000; r=-0.570, P=0.000; r=-0.919, P=0.000; r=-0.781, P=0.000), but with hydroxycamptothecine (HCPT), VCR and 5-FU in the control group (r=-0.915, P=0.000; r=-0.890, P=0.000; r=-0.949, P=0.000). Conclusions: Gastric cancer cells in elderly patients feature stronger MDR, which may be related to high COX-2 expression.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.3
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• pp.837-846
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• 2012

Breast cancer (BCa) is the leading type of cancer in Mexican women. Genetic factors, such as single nucleotide polymorphisms (SNP) of P450 system, have been reported in BCa. In this report, and for the first time in the literature, we analyzed the rs3735684 (7021 G>A), rs11553651 (15016 G>T) and rs56195291 (60020 C>G) polymorphisms in the CYP2W1, 4F11 and 8A1 genes in patients with BCa and in healthy Mexican women to identify a potential association between these polymorphisms and BCa risk. Patients and controls were used for polymorphism analysis using an allelic discrimination assay with TaqMan probes and confirmed by DNA sequencing. Links with clinic-pathological characteristics were also analyzed. Statistical analysis was performed using the standard ${\chi}^2$ or Fisher exact test statistic. No significant differences were observed in the distributions of CYP2W1 (OR 8.6, 95%CI 0.43-172.5 P>0.05; OR 2.0, 95%CI 0.76-5.4, P>0.05) and CYP4F11 (OR 0.3, 95%CI 0.01-8.4 P>0.05) genotypes between the patients and controls. Only the CYP8A1 CC genotype was detected in patients with BCa and the controls. All polymorphism frequencies were in Hardy-Weinberg Equilibrium (HWE) in the controls (P>0.05). We found a significant association between BCa risk and smoking, use of oral contraceptives or hormonal replacement therapy (HRT), obesity, hyperglycemia, chronic diseases, family history of cancer and menopausal status in the population studied (P<0.05). Tobacco, oral contraceptive or HRT, chronic diseases and obesity or overweight were strongly associated with almost eight, thirty-five, nine and five-fold increased risk for BCa. Tobaco, obesity and hyperglycemia significantly increased the risk of BCa in the patients carrying variant genotypes of CYP2W1 (P<0.05). These results indicate that the CYP2W1 rs3735684, CYP4F11 rs11553651 and CYP8A1 rs56195291 SNPs are not a key risk factor for BCa in Mexican women. This study did not detect an association between the CYP2W1, 4F11 and 8A1 genes polymorphisms and BCa risk in a Mexican population. However, some clinico-pathological risk factors interact with CYP2W1 genotypes and modifies susceptibility to BCa.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.59 no.3
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• pp.263-281
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• 2014

Transcription factors are essential for the regulation of gene expression in plant. They are binding to either enhancer or promoter region of DNA adjacent to the gene and are related to basal transcription regulation, differential enhancement of transcription, development, response to intercellular signals or environment, and cell cycle control. The mechanism in controlling gene expression of transcription can be understood through the assessment of the complete sequence for the maize genome. It is possible that the maize genome encodes 4,000 or more transcription factors because it has undergone whole duplication in the past. Previously, several transcription factors of maize have been characterized. In this review article, the transcription factors were selected using Pfam database, including many family members in comparison with other family and listed as follows: ABI3/VP1, AP2/EREBP, ARF, ARID, AS2, AUX/IAA, BES1, bHLH, bZIP, C2C2-CO-like, C2C2-Dof, C2C2-GATA, C2C2-YABBY, C2H2, E2F/DP, FHA, GARP-ARR-B, GeBP, GRAS, HMG, HSF, MADS, MYB, MYB-related, NAC, PHD, and WRKY family. For analyzing motifs, each amino acid sequence has been aligned with ClustalW and the conserved sequence was shown by sequence logo. This review article will contribute to further study of molecular biological analysis and breeding using the transcription factor of maize as a strategy for selecting target gene.

• The Korean Journal of Mycology
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• v.40 no.4
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• pp.224-228
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• 2012

In order to screen interactor(s) of the Aspergillus nidulans ${\alpha}$-COP of COPI vesicle, we performed the yeast two hybrid screening by using the gene for A. nidulans ${\alpha}$-COP as a bait and identified ${\varepsilon}$-COP of the COPI vesicle as an interacting protein. The A. nidualns gene for the ${\varepsilon}$-COP was designated $aneA^+$ ($\underline{A.}$ $\underline{n}$idulans $\underline{e}$psi-lone-COP), which encoded 296 amino acid residues with high level of identity with orthologs from other fungi. Domain analyses with yeast two-hybrid system suggested that the interaction between ${\alpha}$-COP and ${\varepsilon}$-COP relied on the C-terminus of both proteins, and that the N-terminal WD domian of ${\alpha}$-COP and the TPR region of ${\varepsilon}$-COP were not essential but required for the enhancement of the interaction. These results indicate that the interaction mode between ${\alpha}$-COP and ${\varepsilon}$-COP of COPI vesicle is evolutionarily well conserved in eukaryotes.

• Journal of Life Science
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• v.20 no.6
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• pp.934-939
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• 2010

We have previously reported recombinant productions of bacteriocins using yeast expression plasmid pAUR123, which contains the alcohol dehydrogenase (ADH) promoter, in Saccharomyces cerevisiae cells and their antibacterial activities. In order to improve the antibacterial activities of bacteriocidal yeast cells, a strong glyceraldehyde phosphate dehydrogenase (GPD) promoter gene of S. cerevisiae was amplified and inserted upstream into bacteriocin genes such as the OR-7, Subpeptin JM4-A or JM4-B gene in the corresponding recombinant yeast plasmid. Yeast cells transformed by the recombinant plasmid containing the GPD promoter represented higher antibacterial activities against both Gram positive B. subtilis and Gram negative E. coli cells compared to those transformed by the corresponding recombinant plasmid containing the ADH promoter. Thus, yeast cells harboring the recombinant plasmid containing the GPD promoter constructed in this study could be applied in the food preservative or animal feed industries.

• Journal of dental hygiene science
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• v.1 no.1
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• pp.7-11
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• 2001

Streptococcus mutans is one of the primary bacteria that cause dental caries which further result in plaque build up. Acid production resulted from carbohydrate metabolism can threaten survival of the bacteria. However some populations of S. mutans which are exposed to low acidic condition for a period of time would develop resistance and tolerance of cells to acidity that will enhance the chance of survival. Similar acid tolerances has been reported in case of Salmonella enterica serovar typhimurium, E. coli, Shigella flexneri. These acid tolerance responses(ATR) have been evolved in a similar manner as S. mutans. The protein produced in acidic condition has been proven to be important for ATR and confirmed by using chloramphenicol procedure. We hypothesize here that proteins synthesized in response to acid shock and other elements are important for ATR of cells. In this study we have confirmed that S. mutans developed acid tolerance and resistance against anaerobic condition. Mutational DNA analysis responsible for acid tolerance should be additionally required in the future. Since the development of acid tolerance that is essential for the survival of S. mutans and development of dental caries, ATR of S. mutans shoule be farther to prevent dental caries.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.303-307
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• 2010

Acinetobacter baumannii 1625, a clinical isolate identified by Vitek and 16S rDNA sequence, showed an extended resistance to most ${\beta}$-lactams including imipenem, kanamycin, gentamicin, tobramycin, and cephalosporins of the third and fourth generations, and produced metallo-${\beta}$-lactamase (MBL) of IMP-1 type which is rare in Korea. The isolate contained a class 1 integron of about 2.5 kb in size and the integron included accA4 (aminoglycoside resistance gene), $bla_{IMP-1}$ (carbapenem resistance gene), and $bla_{OXA-2}$ (extended-spectrum ${\beta}$-lactam resistance gene) gene cassettes in order. The coexistence of IMP-1 type and OXA-2 type ${\beta}$-lactamase gene cassettes in an integron has not been reported in Korea. The transformed integron rendered the E. coli transformant resistant more than eight folds against imipenem, ampicilin, piperacillin, cefazolin, cefoperazone, and aztreonam comparing to the reference strain. This study clearly showed that the extended multi-drug resistance of A. baumannii 1625 was mainly due to the integron.