• BMB Reports
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• 제41권10호
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• pp.739-744
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• 2008

Turnip yellow mosaic virus (TYMV) is a positive strand RNA virus that infects mainly Cruciferae plants. In this study, the TYMV genome was modified by inserting an extra subgenomic RNA promoter and a multiple cloning site. This modified TYMV was introduced into Nicotiana benthamiana using a Agrobacterium-mediated T-DNA transfer system (agroinfiltration). When a gene encoding $\beta$-glucuronidase or green fluorescent protein was expressed using this modified TYMV as a vector, replication of the recombinant viruses, especially the virus containing $\beta$-glucuronidase gene, was severely inhibited. The suppression of replication was reduced by co-expression of viral silencing suppressor genes, such as tombusviral p19, closteroviral p21 or potyviral HC-Pro. As expected, two subgenomic RNAs were produced from the recombinant TYMV, where the larger one contained the foreign gene. An RNase protection assay revealed that the recombinant subgenomic RNA was encapsidated as efficiently as the genuine subgenomic RNA.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.159-161
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• 2002

Bacteriophage lambda integrase carries out the site-specific recombination of lambda. Integrase contains two DNA binding domains with distinct sequence specificity, namely arm-type binding and core-type binding domains. The amino-terminal arm-binding domain is structurally related to the three-stranded $\beta-sheet$ family of DNA-binding domains. Integrase binding to the high affinity arm-type site by the amino-terminal domain facilitates Int binding to the low affinity core-type site, where the cleavage and strand exchange occurs. The amino-terminal domain of Int also modulates the core-binding and catalysis through intramolecular domain-domain interaction and/or intermolecular interactions between Int monomers. In addition, the amino-terminal domain interacts cooperatively with excisionase during excision. This indicates that amino-terminal domain of Int plays an important role in formation of proper higher-order nucleoprotein structure required for lambda site-specific recombination.

• Asian-Australasian Journal of Animal Sciences
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• 제29권3호
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• pp.315-320
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• 2016

Porcine beta-defensin-1 (PBD-1) gene plays an important role in the innate immunity of pigs. The peptide encoded by this gene is an antimicrobial peptide that has direct activity against a wide range of microbes. This peptide is involved in the co-creation of an antimicrobial barrier in the oral cavity of pigs. The objective of the present study was to detect polymorphisms, if any, in exon-1 and exon-2 regions of PBD-1 gene in Large White Yorkshire (LWY) and native Ankamali pigs of Kerala, India. Blood samples were collected from 100 pigs and genomic DNA was isolated using phenol chloroform method. The quantity of DNA was assessed in a spectrophotometer and quality by gel electrophoresis. Exon-1 and exon-2 regions of PBD-1 gene were amplified by polymerase chain reaction (PCR) and the products were subjected to single strand conformation polymorphism (SSCP) analysis. Subsequent silver staining of the polyacrylamide gels revealed three unique SSCP banding patterns in each of the two exons. The presence of single nucleotide polymorphisms (SNPs) was confirmed by nucleotide sequencing of the PCR products. A novel SNP was found in the 5'-UTR region of exon-1 and a SNP was detected in the mature peptide coding region of exon-2. In exon-1, the pooled population frequencies of GG, GT, and TT genotypes were 0.67, 0.30, and 0.03, respectively. GG genotype was predominant in both the breeds whereas TT genotype was not detected in LWY breed. Similarly, in exon-2, the pooled population frequencies of AA, AG, and GG genotypes were 0.50, 0.27, and 0.23, respectively. AA genotype was predominant in LWY pigs whereas GG genotype was predominant in native pigs. These results suggest that there exists a considerable genetic variation at PBD-1 locus and further association studies may help in development of a PCR based genotyping test to select pigs with better immunity.

• 대한수의학회지
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• 제38권3호
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• pp.606-613
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• 1998

Cadmium is one of the well-known environmental toxicants and induces cancer in rodents and human, but its carcinogenic mechanism has not been well demonstrated until now. Genotoxic effects of cadmium in Salmonella typhimurium TA98, TA100 and TA1535/pSK1002 or in WB-F344 rat liver epithelial cells were investigated to elucidate the tumor initiating effects of cadmium. TA98, TA100 and TA1535/pSK1002 tester strains were used to detect frameshift mutation, base-pair mutation and SOS repair response, respectively, in Salmonella mutation test. Reverse mutations from histidine to $histidin^+$ of Salmonella typhimurium TA98 and TA100 by $CdCl_2$ were not significantly different from control up to the maximum doses ($100{\mu}M$ and $200{\mu}M$ in TA98 and TA100, respectively) at which non-cytotoxicity was observed. DNA SOS repair responses(${\beta}$-galactosidase activity) generally did not show significant increases compared to control in both of the conditions with or without metabolic activation in Salmonella typhimurium TA1535/pSK1002 by $CdCl_2$. But the activities of ${\beta}$-galactosidase by $400{\mu}M$ of $CdCl_2$ in metabolic activation condition and by 130 and $400{\mu}M$ of $CdCl_2$ in non-metabolic activation condition were more decreased than those of control. DNA single strand breaks for 4hrs were observed only in WB-F344 rat liver epithelial cells treated with $200{\mu}M$ of $CdCl_2$. As a conclusion, $CdCl_2$ did not induce gene mutation in microbials but induce DNA single strand breaks in rat liver epithelial cells.

• Bulletin of the Korean Chemical Society
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• 제23권12호
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• pp.1744-1748
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• 2002

Trifluoroacetate anion as a connector has been studied on $AgCF_3CO_2$ with 3,3'-$Py_2X$(X=O vs S) produces 1 : 1 adducts of [Ag($CF_3CO_2$)(3,3'-$Py_2X<$)]. Crystallographic characterization of [Ag($CF_3CO_2$)(3,3'-$Py_2X$)](monoclinic $P2_1$a=7.383(1)$\AA$b=19.801(3)$\AA$c=9.297(3)$\AA$,$\beta$=$100.26(2)^{\circ}$,V=1337.4(5) $\AA^3$, Z=2, R=0.0386) reveals that the 3,3'-$Py_2O$ spacer connects two silver ions to give a single strand and that the single strands are linked via the trifluoroacetate anions in an "up and down even-bridge" to give an elegant molecular grid. The framework of [$Ag(CF_3CO_2)(3,3'-Py_2X)$](monoclinic $P2_1/c$a=8.331(2)$\AA$b=14.010(2)$\AA$,c=11.926(3 $\AA$$\beta$=$93.70(2)^{\circ}$=1385.1(6)$\AA^3$, Z=4, R=0.0589) is a single-strand. The single strands are connected via the trifluoroacetate anions in a double-bridge, resulting in a typical molecular chicken-wire. The trifluoroacetate anion as a connector appears to be primarily associated with its moderately coordinating ability. Their structural features have been discussed based on the anion exchangeability. Thermal analyses indicate that the compounds are stable up to approximately $200^{\circ}C$.

• 대한의생명과학회지
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• 제15권1호
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• pp.1-8
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• 2009

Human genomic DNA is continuously attacked by oxygen radicals originated from cellular metabolic processes and numerous environmental carcinogens. 2-deoxyribonolactone (dL) is a major type of oxidized abasic (AP) lesion implicated in DNA strand scission, mutagenesis, and formation of covalent DNA-protein crosslink (DPC) with DNA polymerase (Pol) ${\beta}$. We show here that human DNA polymerase (Pol)${\iota}$ and mitochondrial $Pol{\gamma}$ give rise to stable DNA-protein crosslink (DPC) formation that is specifically mediated by dL lesion. $Pol{\gamma}$ mediates DPC formation at the incised dL residue by its 5'-deoxyribose-5-phosphate (dRP) lyase activity, while $Pol{\gamma}$ cross links with dL thorough its intrinsic dRP lyase and AP lyase activities. Reactivity in forming dL-mediated DPC was significantly higher with $Pol{\gamma}$ than with $Pol{\iota}$. DPC formation by $Pol{\gamma}$, however, can be reduced by an accessory factor of $Pol{\gamma}$ holoenzyme that may attenuate deleterious effects of crosslink adducts on mitochondrial DNA. Comparative kinetic analysis of DPC formation showed that the rate of DPC formation with either $Pol{\iota}$ or $Pol{\gamma}$ was lower than that with $Pol{\beta}$. These results revealed that the activity of catalytic lyase in DNA polymerases determine the efficiency of DPC formation with dL damages. Irreversible crosslink formation of such DNA polymerases by dL lesions may result in a prolonged strand scission and a suicide of DNA repair proteins, both of which could pose a threat to the genetic and structural integrity of DNA.

• 대한본초학회지
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• 제22권1호
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• pp.7-12
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• 2007

Objectives : In Alzheimer's disease(AD), free radical oxidative stress caused by amyloid beta-peptide may lead to DNA damage, neuronal dysfunction, neurotoxicity and cell death, Hwangryunhaedok-tang(HHT) is traditionally used for the treatment of pyrogenetic diseases. To develop a new anti-AD drug from natural herb, HHT was selected and extracted in this study. Methods : The antioxidant activities of HHT water extract powder were examined by hydroxyl radical-induced DNA strand nicking assay, and antioxidative enzymes expression assay in H4IIE cell. In addition, HHT was examined for the inhibitory effect on the acetylcholinesterase(AChE) using by Ellman's coupled assay. Results: The HHT exhibit DNA protective effect in the hydroxyl radical-induced DNA Strand nicking assay, mRNA expression of superoxide dismutase and glutathione peroxidase were recovered at a normal level by HHT treatment in H4IIE cell. Furthermore, water extract of HHT showed inhibitory effect on AChE activity. Conclusion : These results suggest that HHT may be effective in delaying and preventing AD progression related to the free radical-induced DNA damage and AChE activity.

• BMB Reports
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• 제39권3호
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• pp.284-291
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• 2006

In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the $\beta$-strand1 to the $\alpha$-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of $\alpha$-, $\beta$-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a $\beta$-toxin that competes with the depressant insect toxins for binding to $Na^+$ channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded $\beta$-sheet and a stretch of $\alpha$-helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.

• Smart Structures and Systems
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• 제19권3호
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• pp.269-277
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• 2017

Recently, there has been significant interest in structural health monitoring for civil engineering applications. In this research, a specially designed tendon, proposed by embedding FBG sensors into the center king cable of a 7-wire strand tendon, was applied for long-term health monitoring of tensile forces on a ground anchor. To make temperature independent sensors, the effective temperature compensation of FBG sensors must be considered. The temperature sensitivity coefficient ${\beta}^{\prime}$ of the FBG sensors embedded tendon was successfully determined to be $2.0{\times}10^{-5}^{\circ}C^{-1}$ through calibrated tests in both a model rock body and a laboratory heat chamber. Furthermore, the obtained result for ${\beta}^{\prime}$ was formally verified through the ground temperature measurement test, expectedly. As a result, the ground temperature measured by a thermometer showed good agreement compared to that measured by the proposed FBG sensor, which was calibrated considering to the temperature sensitivity coefficient ${\beta}^{\prime}$. Finally, four prototype ground anchors including two tension ground anchors and two compression ground anchors made by replacing a tendon with the proposed smart tendon were installed into an actual slope at the Yeosu site. Tensile forces, after temperature compensation was taken into account using the verified temperature sensitivity coefficient ${\beta}^{\prime}$ and ground temperature obtained from the Korean Meteorological Administration (KMA) have been monitored for over one year, and the results were very consistent to those measured from the load cell, interestingly.

• BMB Reports
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• 제44권2호
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• pp.118-122
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• 2011

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.