• BMB Reports
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• v.56 no.6
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• pp.347-352
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• 2023

The protein family of poly (ADP-ribose) polymerases (PARPs) is comprised of multifunctional nuclear enzymes. Several PARP inhibitors have been developed as new anticancer drugs to combat resistance to chemotherapy. Herein, we characterized PARP4 mRNA expression profiles in cisplatin-sensitive and cisplatin-resistant ovarian cancer cell lines. PARP4 mRNA expression was significantly upregulated in cisplatin-resistant ovarian cancer cell lines, and this upregulation was associated with the hypomethylation of specific cytosine-phosphate-guanine (CpG) sites (cg18582260 and cg17117459) on its promoter. Reduced PARP4 expression was restored by treating cisplatin-sensitive cell lines with a demethylation agent, implicating the epigenetic regulation of PARP4 expression by promoter methylation. Depletion of PARP4 expression in cisplatin-resistant cell lines reduced cisplatin chemoresistance and promoted cisplatin-induced DNA fragmentation. The differential mRNA expression and DNA methylation status at specific PARP4 promoter CpG sites (cg18582260 and cg17117459) according to cisplatin responses, was further validated in primary ovarian tumor tissues. The results showed significantly increased PARP4 mRNA expressions and decreased DNA methylation levels at specific PARP4 promoter CpG sites (cg18582260 and cg17117459) in cisplatin-resistant patients. Additionally, the DNA methylation status at cg18582260 CpG sites in ovarian tumor tissues showed fairly clear discrimination between cisplatin-resistant patients and cisplatin-sensitive patients, with high accuracy (area under the curve = 0.86, P = 0.003845). Our findings suggest that the DNA methylation status of PARP4 at the specific promoter site (cg18582260) may be a useful diagnostic biomarker for predicting the response to cisplatin in ovarian cancer patients.

• Journal of Environmental Science International
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• v.12 no.2
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• pp.217-225
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• 2003

Samples of size-fractionated PM10 (airborne particulate matter with aerodynamic diameter less than $10\mu\textrm{m}$) were collected at an urban site in Jeju city from May to September 2002. The mass concentration and chemical composition of the samples were measured. The data sets were then applied to the CMB receptor model to estimate the source contribution of PM10 in Jeju area. The average PM10 mass concentration was 28.80$\mu\textrm{g}/m^3$ ($24.6~33.49\mu\textrm{g}/m^3$), and the FP (fine particle with aerodynamic diameter less than $2.l\mu\textrm{m}$ fraction in PM10 was approximately 8% higher than the CP (coarse particle with aerodynamic diameter greater than $2.l\mu\textrm{m}$ and less than $10\mu\textrm{m}$ fraction in PM10. The CP composition was obviously different from the FP composition, that is, the most abundant water soluble species was nitrate ion in the FP, but sulfate ion in the CP. Also sulfur was the most dominant element in the FP, however, sodium was that in the CP. From CMB receptor model results, it was found that road dust was the largest contributor to the CP mass concentration (45% of the CP) and ammonium nitrate, domestic boiler, and marine aerosol were major sources to the CP mass. However, the secondary aerosol was the most significant contributor to the FP mass concentration (45% of the FP). In this study, it was suggested that the contributions of soil dust and gasoline vehicle became very low due to collinearity with road dust and diesel vehicle, respectively.

• Journal of Life Science
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• v.11 no.2
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• pp.108-110
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• 2001

The E. coli expression system to overproduce a harmful protein, carboxypeptidase Taq was developed. Since expression plasmid pCK305N containing the colicin promoter already has the initiation codon on the restriction site, the initiation codon of the CPase Taq gene was removed. Expression plasmid pCP4-col includes the entire CPase Taq gene, which is directed by the colicin promoter. E. coli cells harboring pCP-col produced a high amount of the enzyme when they were cultured in the present of mitomycin C (0.4 ${\mu}g$/ml). An amount of purified enzyme produced by pCP4-col directed by the colicin promoter was 10.5 mg. This result indicated that the novel E. coli expression system controlled by the colicin promoter could produce almost twice amounts of CPase Taq than the conventional system controlled by the tart promoter.

• Genomics & Informatics
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• v.9 no.4
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• pp.194-196
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• 2011

Promoter prediction is a very important problem and is closely related to the main problems of bioinformatics such as the construction of gene regulatory networks and gene function annotation. In this context, we developed an integrated promoter prediction program using hybrid methods, PromoterWizard, which can be employed to detect the core promoter region and the transcription start site (TSS) in vertebrate genomic DNA sequences, an issue of obvious importance for genome annotation efforts. PromoterWizard consists of three main modules and two auxiliary modules. The three main modules include CDRM (Composite Dependency Reflecting Model) module, SVM (Support Vector Machine) module, and ICM (Interpolated Context Model) module. The two auxiliary modules are CpG Island Detector and GCPlot that may contribute to improving the predictive accuracy of the three main modules and facilitating human curator to decide on the final annotation.

• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2087-2097
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• 2016

Most cold-adapted enzymes possess higher $K_m$ and $k_{cat}$ values than those of their mesophilic counterparts to maximize the reaction rate. This characteristic is often ascribed to a high structural flexibility and improved dynamics in the active site. However, this may be less convincing to cold-adapted metabolic enzymes, which work at substrate concentrations near $K_m$. In this respect, cold adaptation of a shikimate kinase (SK) in the shikimate pathway from psychrophilic Colwellia psychrerythraea (CpSK) was characterized by comparing it with a mesophilic Escherichia coli homolog (EcSK). The optimum temperatures for CpSK and EcSK activity were approximately $30^{\circ}C$ and $40^{\circ}C$, respectively. The melting points were $33^{\circ}C$ and $45^{\circ}C$ for CpSK and EcSK, respectively. The ${\Delta}G_{H_2O}$ (denaturation in the absence of denaturing agent) values were 3.94 and 5.74 kcal/mol for CpSK and EcSK, respectively. These results indicated that CpSK was a cold-adapted enzyme. However, contrary to typical kinetic data, CpSK had a lower $K_m$ for its substrate shikimate than most mesophilic SKs, and the $k_{cat}$ was not increased. This observation suggested that CpSK may have evolved to exhibit increased substrate affinity at low intracellular concentrations of shikimate in the cold environment. Sequence analysis and homology modeling also showed that some important salt bridges were lost in CpSK, and higher Arg residues around critical Arg 140 seemed to increase flexibility for catalysis. Taken together, these data demonstrate that CpSK exhibits characteristics of cold adaptation with unusual kinetic parameters, which may provide important insights into the cold adaptation of metabolic enzymes.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.11
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• pp.1559-1567
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• 2012

The objective of this study was to evaluate ruminal degradability and intestinal digestibility of crude protein (CP) and amino acids (AA) in hempseed cake (HC) that were moist heat treated at different temperatures. Samples of cold-pressed HC were autoclaved for 30 min at 110, 120 or $130^{\circ}C$, and a sample of untreated HC was used as the control. Ruminal degradability of CP was estimated, using the in situ Dacron bag technique; intestinal CP digestibility was estimated for the 16 h in situ residue using a three-step in vitro procedure. AA content was determined for the HC samples (heat treated and untreated) of the intact feed, the 16 h in situ residue and the residue after the three-step procedure. There was a linear increase in RUP (p = 0.001) and intestinal digestibility of RUP (p = 0.003) with increasing temperature during heat treatment. The $130^{\circ}C$ treatment increased RUP from 259 to 629 g/kg CP, while intestinal digestibility increased from 176 to 730 g/kg RUP, compared to the control. Hence, the intestinal available dietary CP increased more than eight times. Increasing temperatures during heat treatment resulted in linear decreases in ruminal degradability of total AA (p = 0.006) and individual AA (p<0.05) and an increase in intestinal digestibility that could be explained both by a linear and a quadratic model for total AA and most individual AA (p<0.05). The $130^{\circ}C$ treatment decreased ruminal degradability of total AA from 837 to 471 g/kg, while intestinal digestibility increased from 267 to 813 g/kg of rumen undegradable AA, compared with the control. There were differences between ruminal AA degradability and between intestinal AA digestibility within all individual HC treatments (p<0.001). It is concluded that moist heat treatment at $130^{\circ}C$ did not overprotect the CP of HC and could be used to shift the site of CP and AA digestion from the rumen to the small intestine. This may increase the value of HC as a protein supplement for ruminants.

• Journal of Pharmaceutical Investigation
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• v.24 no.3
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• pp.155-165
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• 1994

Some mucoadhesive polymers such as hydroxypropylcelluose (HPC) and carbopol-934 (CP) have been employed for the preparation of mucoadhesive polymeric systems, and their physical properties including mucoadhesion, swelling, and drug release were evaluated. A new simple experimental technique that can quantitatively measure the bioadhesive properties of various polymeric systems has been developed by the methods of detachment force test. As the polymeric systems, the discs of freeze-dried HPC/CP solid dispersions were prepared. The mucosa used in these tests were upper, middle, and lower parts of small intestine of male rats weighing $300{\sim}350\;g$. Detachment forces were increased as the mole fraction of CP increased in discs of HPC/CP solid dispersions. In the points of intestinal site dependence of mucoadhesion, the solid dispersions revealed non-specific mucoadhesion to the intestine. Swelling and drug release characteristics of mucoadhesive polymeric systems were studied extensively to find out the feasibility for the oral controlled delivery systems. Swelling ratio, expressed as the final height/initial height, has been determined in various pH buffer solutions. Hydrochlorothiazide (HCT) was employed as a model drug for release study. Apparent swelling and drug release rate constants, $K_s$ and $K_r$ respectively, were obtained from the square-root time plot of either swelling ratio or released amount of drug, particularly for the time periods before reaching the equilibrium. As a result, the swelling ratio of HPC/CP solid dispersions was increased as the weight percentage of CP increased. Similarly, the release of HCT from the solid dispersions was dependent on pH changes and CP contents, resulted in the slower release of HCT with the increases of pH and CP contents.

• The Journal of the Korea Contents Association
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• v.13 no.8
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• pp.466-473
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• 2013

Gene expression is regulated by a wide range of mechanisms at the DNA sequence level. In addition, gene expression is also regulated by epigenetic mechanisms through DNA methylation, histone modification, and ncRNA. To understand the regulation of gene expression at the epigenetic level, we constructed aging related gene database and analyzed epigenetic properties that are focused on DNA methylation. The DNA methylation of promoter or upstream region of the genes induces to repress the gene expression. We compared and analyzed distribution between whole human genes and aging related genes in the epigenetic properties such as CGI distribution, methylation motif pattern, and TFBS (transcription factor binding site) distribution. In contrast to methylation motif pattern, CGI and TFBS distributions are positively correlated with epigenetic regulation of aging related gene expression. In this study, the epigenetic data about DNA methylation of the aging genes will provide us to understand phenomena of the aging and epigenetic mechanism for regulation of aging related genes.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.76.2-77
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• 2003

The complete nucleotide sequences of genomic RNA of an isolate of soybean mosaic virus (SMV-CN18), which has ability to overcome Rsv resistance of soybean, have been determined. A large open reading frame encodes a polyprotein of 3068 amino acids with a predicted Mr of 350 kDa. Based on comparison with the proposed cleavage site of other potyviral polyproteins, nine mature proteins are predicted as a following order, P1, HC-Pro, P3, CI, 6K, VPg, NIa, NIb and coat protein (CP). The mature proteins of the strain share various amino acid identity with known SMV-G2, -G7 and -N strain, with the greatest variability occurring in the P1 (91 ％, 88 ％, 96％)and the lowest variability in the CP (100 ％, 99 ％, 100 ％). In addition, 5' untranslated region determined by 5' RACE is much more various than any coding regions. Difference in amino acid sequences throughout the genome is discussed in relation to resistance and susceptibility of soybean cultivars to SMV-CNl8.

• Asian-Australasian Journal of Animal Sciences
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• v.3 no.4
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• pp.323-330
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• 1990

Two experiments were conducted to evaluate the effect of processing and method of ensiling on the digestion and utilization of high moisture barley (HMB) in cattle. In experiment 1, four Holstein heifers were assigned in a Latin square design to diets containing 70% barley, 25% alfalfa hay and 5% supplement on a dry matter (DM) basis. Diets differed only in the type of barley fed: rolled dry barley (R-DB), rolled HBM (R-HMB), ground HMB (G-HMB) or unprocessed HMB (U-HMB). In experiment 2, three Holstein steers were fed 85.2% barley, 10.2% whole plant barley silage and 4.6% supplement on a DM basis. Again, diets differed only in the type of barley fed: R-DB, rolled HMB from a pit silo (Pit-HMB) or rolled HMB from a Harvestore silo (HAV-HMB). In experiment 1, digestibility coefficients for animals fed R-HMB were significantly higher than observed for U-HMB. While not significant, a similar trend for decreased digestibility was observed for R-DB and G-HMB. Animals fed HMB had significantly lower ruminal propionate concentrations. In addition, the rate of degradation of the degradable DM and crude protein (CP) fractions was slower for HMB than for dry barley. In experiment 2, a trend to lower digestibility coefficients was observed for animal fed R-DB compared to those fed Pit-HMB or HAV-HMB. Ruminal propionate concentrations for animals fed R-DB also tended to be higher than for those fed the HMB diets. Dry matter and CP disappearances from nylon bags was substantially lower for Pit-HMB than for R-DB or HAV-HMB. The results suggest that replacement of dry barley by rolled or unprocessed HMB in the diet of animals fed high grain diets may contribute to a more stable rumen environment.