• Genomics & Informatics
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• v.16 no.2
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• pp.22-29
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• 2018

Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.

• Biomedical Science Letters
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• v.2 no.2
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• pp.175-185
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• 1996

The mitogen-activated protein(MAP) kinase signal transduction pathway represents an important mechanism by which mitogen, such as serum and PMA, regulate cell proliferation and differentiation. Target substrates of the MAP kinase are located within several compartments containing plasma membranes and nucleus. We now report that serum addition induces proliferation of the P388 murine leukemia cell, but PMA does not, while both serum and PMA treatment cause translocation of the MAP kinase, mainly p42$^{mapk}$ isoform, from cytosol into the nucleus, which was monitored by immunoblot analysis using polyclonal anti-ERK1 antibodies. We investigated whether the MAP kinase was capable of phosphorylating c-Jun protein and GST-fusion proteins, the P562$^{kk}$N-terminal peptides (1-77 or 1-123 domain) of the T cell tyrosine kinase, using the partially purified MAP kinase by SP-sephadex C-50, phenyl superose and Mono Q column chromatography. We found that the partially purified MAP kinase was able to phosphorylate c-Jun protein and the GST-fusion protein expressed using E.coli DH5$\alpha$ which is transformed with pGEX-3Xb plasmid vector carrying of p562$^{kk}$N-terminal peptide-encoding DNA. These results imply that tyrosine kinase receptor/Ras/Raf/MAP kinase pathway is a major mechanism for mitogen-induced cell proliferation in P388 murine leukemia cell and that the various MAP kinase isoforms may have their own target substrates located in distinct subcellular compartments.

• The Journal of Korean Medicine
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• v.27 no.1 s.65
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• pp.184-195
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• 2006

Objectives : Betula Platyphylla(BP) is a traditional analgesic, anti-fungal, anti-inflammatory herb used in Chinese 1medicine. However, no information is available to explain its action. In this study. we investigated the anti-inflammatory 1effects of BP to elutidate the molecular pharmacological activity in the ethanol extract of BP(BPE). Methods : We performed WTS assay in lipopolysaccharide (LPS) stimulated RAW264.7 macrophages with BPE. Nitrite was measured by Griess assay, prostaglandin E2 (PGE2) by enzyme-linked immunosorbent assay (ELISA) in LPS induced RAW264.7 macrophages with BPE. Inducible nitric oxide synthase (iNOS) and cyclooxygenase (COX-2) were determined by Western blot. Activation of nuclear factor-kappaB (NF-kB) was measured by electrophoretic mobility shift assay (EMSA). Results : BPE significantly suppressed production of nitric oxide (NO) and PGE2 in LPS-induced RAW264.7 macrophages in a dose-dependent manner. The maximal inhibition rate of NO and PGE2 production by BPE was ca. 88.8% and 93% at the concentration of $100{\mu}g/ml$ (non-cytotoxic concentration), respectively. BPE also decreased iNOS protein and COX-2 protein in LPS-induced RAW264.7 macrophages. EMSA demonstrated that BPE inhibited the DNA binding activity of the NF-kB. Conclusions : These results suggest that BPE inhibits NF-${\kappa}B$-mediated gene expression and downregulates inflammatory mediator production in RAW264.7 macrophages.

• Biomedical Science Letters
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• v.16 no.4
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• pp.229-238
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• 2010

Chicken Mx protein (cMx) induced interferon (IFN) is an antiviral protein to inhibit replication of RNA virus, particularly negative stranded RNA virus, through blockage of transfortation of viral RNA and proteins. In order to determine antiviral effects of cMx from different MHC haplotype chicken, we characterized cMx gene by studying on nucleotide sequencing, antiviral effects to Newcastle disease virus, VSV and MDV, and transcription activities. Three types of eMx genes (2,118 bp) were detected from the different MHC haplotype chickens [B19 (N), B15(F) and B21 (GSP)] chickens, which have showed different susceptible to Marek's disease (MD). Several amino acid substitutions were showed in the cMx. The amino acid 548 and 631 in the cMxs from N and F, chickens susceptible to MD, was Val and Asn which was important on antiviral effects, and showed in resistant cMx. Those in the cMx from GSP, chicken resistant to MD, were same that showed in susceptible cMx. Though every cMx transactivated the expression of the reporter gene, the transcription activation by resistant cMx from N and F was lower compared to that by susceptible cMx from GSP. The decease of the cell growth in the resistant cMx cloned cells was seen in comparison with another cMx clone cells. Replication of NDV and VSV was suppressed in the clones with resistant cMx from N and F. NMx258-transducted cells lack of antiviral effects, and NMx437 or NMx646-transducted cells was showed 60% of antiviral effects compared to NMx705. Mean death time (MDT) and hemaggutination (HA) titer to NDV was long and low in the eggs of N and F lines, but short and high in the egg of GSP line. Interestingly, strong suppression to NDV was observed in the clone with N-Mx and in the eggs of N line. However, the effects of Mx for replication of vvMDV1 have not been. Thus, resistant types of cMx, N- and F-Mx, have showed the anti-viral effects to only RNA virus including NDV and VSV, but not to DNA virus. Antiviral effects of cMx were required whole length of amino acid including Val and Asn in amino acid 548 and 631.

• Journal of Plant Biotechnology
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• v.1 no.1
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• pp.20-30
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• 1999

In order to modify lipid production of Perilla qualitatively as well as quantitatively by genetic engineering, genes involved in carbon metabolism were isolated and characterized. These include acyl-ACP thioesterases from Perilla frutescens and Iris sp., four different $\beta$-ketoacyl- ACP synthases from Perilla frutescens, and two $\Delta$15 a-cyl-ACP desaturases(Pffad7, pffad3). Δ15 acyl-ACP desa turase (Δ15-DES) is responsible for the conversion of linoleic acid (18:2) to $\alpha$-linolenic acid (ALA, 18:3). pffad 3 encodes Δ15 acyl-desaturase which is localized in ER membrane. On the other hand, Pffad7 encodes a 50 kD plastid protein (438 residues), which showed highest sequence similarity to Sesamum indicum fad7 protein. Northern blot analysis revealed that the Pffad7 is highly expressed in leaves but not in roots and seeds. And Pffad3 is expressed throughout the seed developmental stage except very early and fully mature stage. We constructed Pffad7 gene under 355 promoter and Pffad3 gene under seed specific vicillin promoter. Using Pffad7 construct, Perilla, an oil seed crop in Korea, was transformed by Agrobacterium leaf disc method. $\alpha$-linolenic acid contents increased in leaves but decreased in seeds of transgenic Perilla. Currently, we are transforming Perilla with Pffad3 construct to change Perilla seed oil composition. We isolated three ADP-glucose pyrophosphorylase (AGP) genes from Perilla immature seed specific cDNA library. Nucleotide sequence analysis showed that two of three AGP (Psagpl, Psagp2) genes encode AGP small subunit polypeptides and the remaining (Plagp) encodes an AGP large subunit. PSAGPs, AGP small subunit peptide, form active heterotetramers with potato AGP large subunit in E. coli expressing plant AGP genes.

• Molecular & Cellular Toxicology
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• v.2 no.2
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• pp.134-140
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• 2006

Because shipyard workers are involved with various manufacturing process in shipyard industry, and they are exposed to many kinds of hazardous materials. Especially, painting workers were exposed polycyclic aromatic hydrocarbons (PAH). This study was conducted to assess the exposure status of PAH based on job-exposure matrix. We investigated the effect of genetic polymorphism of xenobiotic metabolism enzymes involved in PAH metabolism on levels of urinary metabolite. A total of 93 shipbuilding workers were recruited in this study. Questionnaire variables were age, sex, use of personal protective equipment, smoking, drinking, and work duration. The urinary metabolite was collected in the afternoon and corrected by urinary creatinine concentration. The genotypes of CYP1A1, CYP2E1, GSTM1, GSTT1 and UGT1A6 were investigated by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods with DNA extracted from venous blood. Urinary 1-OHP levels were significantly higher in direct exposured group (spray and touch-up) than indirect exposed group. Urinary 1-OHP, concentration of the high exposure with wild type of UGT1A6 was significantlyhigher than that of the high exposure with other UGT1A6 genotype. In multiple regression analysis of urinary 1-OHP, the regression coefficient of job grade was statistically significant (p<0.05) and UGT1A6 was not significant but a trend (p<0.1). The grade of exposure affected urinary PAH concentration was statistically significant. But genetic polymorphism of xenobiotics metabolism enzymes was not statistically significant. Further investigation of genetic polymorphism with large sample size is needed.

• The Plant Pathology Journal
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• v.34 no.5
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• pp.381-392
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• 2018

Clavibacter michiganensis subsp. michiganesis (Cmm) is a quarantine-worthy pest in $M{\acute{e}}xico$. The implementation and validation of new technologies is necessary to reduce the time for bacterial detection in laboratory conditions and Raman spectroscopy is an ambitious technology that has all of the features needed to characterize and identify bacteria. Under controlled conditions a contagion process was induced with Cmm, the disease epidemiology was monitored. Micro-Raman spectroscopy ($532nm\;{\lambda}$ laser) technique was evaluated its performance at assisting on Cmm detection through its characteristic Raman spectrum fingerprint. Our experiment was conducted with tomato plants in a completely randomized block experimental design (13 plants ${\times}$ 4 rows). The Cmm infection was confirmed by 16S rDNA and plants showed symptoms from 48 to 72 h after inoculation, the evolution of the incidence and severity on plant population varied over time and it kept an aggregated spatial pattern. The contagion process reached 79% just 24 days after the epidemic was induced. Micro-Raman spectroscopy proved its speed, efficiency and usefulness as a non-destructive method for the preliminary detection of Cmm. Carotenoid specific bands with wavelengths at 1146 and $1510cm^{-1}$ were the distinguishable markers. Chemometric analyses showed the best performance by the implementation of PCA-LDA supervised classification algorithms applied over Raman spectrum data with 100% of performance in metrics of classifiers (sensitivity, specificity, accuracy, negative and positive predictive value) that allowed us to differentiate Cmm from other endophytic bacteria (Bacillus and Pantoea). The unsupervised KMeans algorithm showed good performance (100, 96, 98, 91 y 100%, respectively).

• Biomolecules & Therapeutics
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• v.19 no.2
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• pp.187-194
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• 2011

Atherosclerosis and post-angiography restenosis are associated with intimal thickening and concomitant vascular smooth muscle cell (VSMC) proliferation. Obovatol, a major biphenolic component isolated from the Magnolia obovata leaf, is known to have anti-inflammatory and anti-tumor activities. The goal of the present study was to enhance the inhibitory effects of obovatol to improve its potential as a preventive or therapeutic agent in atherosclerosis and restenosis. Platelet-derived growth factor (PDGF)-BB-induced proliferation of rat aortic smooth muscle cells (RASMCs) was examined in the presence or absence of a newly synthesized obovatol derivative, OD78. The observed anti-proliferative effect of OD78 was further investigated by cell counting and [$^3H$]-thymidine incorporation assays. Treatment with 1-4 ${\mu}M$ OD78 dose-dependently inhibited the proliferation and DNA synthesis of 25 ng/ml PDGF-BB-stimulated RASMCs. Accordingly, OD78 blocked PDGF-BB-induced progression from the $G_0/G_1$ to S phase of the cell cycle in synchronized cells. OD78 decreased the expression levels of CDK4, cyclin E, and cyclin D1 proteins, as well as the phosphorylation of retinoblastoma protein and proliferating cell nuclear antigen; however, it did not change the CDK2 expression level. In addition, OD78 inhibited downregulation of the cyclin-dependent kinase inhibitor (CKI) $p27^{kip1}$. However, OD78 did not affect the CKI $p21^{cip1}$ or phosphorylation of early PDGF signaling pathway. These results suggest that OD78 may inhibit PDGF-BB-induced RASMC proliferation by perturbing cell cycle progression, potentially through $p27^{kip1}$ pathway activation. Consequently, OD78 may be developed as a potential anti-proliferative agent for the treatment of atherosclerosis and angioplasty restenosis.

• Journal of Plant Biotechnology
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• v.30 no.3
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• pp.281-291
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• 2003

In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is the most prevalent technique to rapidly identify a large number of proteome analysis. However, the conventional Western blotting/sequencing technique has been used in many laboratories. As a first step to efficiently construct protein cata-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein sports are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins(i, e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 45% of total rice cDNA have been deposited in the EMBL database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that tuned out to be calreticulin, gibberellin-binding protein, which is ribulose-1.5-bisphosphate carboxylase/oxygense active in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins(http://genome.c.kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Also, the information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful be in the plant molecular breeding.

• The Journal of the Korean Society for Microbiology
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• v.35 no.3
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• pp.263-271
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• 2000

A clinical isolate of Klebsiella pneumoniae K7746 produced the extended-spectrum ${\beta}$-lactamase (ESBL) SHV-12. A 6.6 kb BamHI fragment containing the $bla_{SHV-12}$ gene of K7746 strain was cloned into pCRScriptCAM vector resulting in the recombinant plasmid p7746-Cl. The restriction map of 3.6 kb inserted DNA and sequences immediately surrounding $bla_{SHV-12}$ of p7746-C1 were homologous to plasmid pMPA2a carrying $bla_{SHV-2a}$. In addition, both $bla_{SHV-12}$ and $bla_{SHV-2a}$ were expressed from a common hybrid promoter made of the -35 region derived from the left inverted repeat of IS26 and the -10 region from the $bla_{SHV}$ promoter itself. The results indicate that $bla_{SHV-12}$ and $bla_{SHV-2a}$ may have evolved from a common ancestor in the sequential order of $bla_{SHV-2a}$ first, followed by $bla_{SHV-12}$. Furthermore, by the PCR mapping method using primers corresponding to the IS26 and $bla_{SHV}$, the association between IS26 and $bla_{SHV}$ was studied in 12 clinical isolates carrying $bla_{SHV-2a}$, 27 clinical isolates carrying $bla_{SHV-12}$, and 5 reference strains carrying $bla_{SHV-1}$ to $bla_{SHV-5}$. All 39 strains carrying $bla_{SHV-2a}$ or $bla_{SHV-12}$ were positive by the PCR, providing confirmative evidence that IS26 has been involved in the evolution and dissemination of $bla_{SHV-2a}$ and $bla_{SHV-12}$. But 5 reference strains carrying $bla_{SHV-1}$ to $bla_{SHV-5}$ were negative by the PCR. Therefore, we concluded that the molecular evolutionary pathway of $bla_{SHV-2a}$ and $bla_{SHV-12}$ may be different from that of other $bla_{SHV-ESBL}$, e.g., $bla_{SHV-2}$, $bla_{SHV-3}$, $bla_{SHV-4}$, and $bla_{SHV-5}$.