• Bulletin of the Korean Chemical Society
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• v.28 no.3
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• pp.386-390
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• 2007

By use of a simple two-point extrapolation scheme estimating the correlation energies of the molecules along with the basis sets specifically targeted for extrapolation, we have shown that the MP2 basis set limit binding energies of large hydrogen-bonded complexes can be accurately predicted with relatively small amount of computational cost. The basis sets employed for computation and extrapolation consist of the smallest correlation consistent basis set cc-pVDZ and another basis set made of the cc-pVDZ set plus highest angular momentum polarization functions from the cc-pVTZ set, both of which were then augmented by diffuse functions centered on the heavy atoms except hydrogen in the complex. The correlation energy extrapolation formula takes the (X+1)-3 form with X corresponding to 2.0 for the cc-pVDZ set and 2.3 for the other basis set. The estimated MP2 basis set limit binding energies for water hexamer, hydrogen fluoride pentamer, alaninewater, phenol-water, and guanine-cytosine base pair complexes of nucleic acid by this method are 45.2(45.9), 36.1(37.5), 10.9(10.7), 7.1(6.9), and 27.6(27.7) kcal/mol, respectively, with the values in parentheses representing the reference basis set limit values. A comparison with the DFT results by B3LYP method clearly manifests the effectiveness and accuracy of this method in the study of large hydrogen-bonded complexes.

• Mass Spectrometry Letters
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• v.4 no.4
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• pp.67-70
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• 2013

The Cu-binding site in the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex was investigated. The tandem mass (MS/MS) spectra of the [$[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ parent ion showed $[dCMP{\cdot}Cu{\cdot}H_2PO_4+CONH]^{1-}$ fragment ions. Therefore, we propose that the Cu cation is simultaneously coordinated to the phosphate site and cytosine moiety in the stable geometry of the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex. Three geometries for the complex were considered in an attempt to optimize the structure of the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex. The ab initio calculations were performed at the $B3LYP/6-311G^{**}$ level.

• Korean Journal of Veterinary Research
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• v.46 no.4
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• pp.355-361
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• 2006

Porcine epidemic diarrhea virus (PEDV) strain Chinju99, which was previously isolated from piglets suffering from severe diarrhea was used to characterize the membrane (M) protein gene to establish the molecular information, and the results will be useful in elucidating concepts related to molecular pathogenesis and antigenic structures of PEDV isolates. The Chinju99 M gene generated by reverse transcription and polymerase chain reaction (RT-PCR) consisted of 681 bases containing 22.3% adenine, 22.3% cytosine, 23.1% guanine and 32.3% thymine nucleotides, and the GC content was 45.4%. It had some nucleotide mismatches from M gene of other PEDV strains, such as CV777, Br1/87, KPEDV-9, JMe2, JS2004-2 and LJB-03 with 97-99% nucleotide sequence homology to these strains. Also, it encoded a protein of 226 amino acids, which had some mismatches from those of CV777, Br1/87, KPEDV-9, JMe2, JS20004-2 and LJB-03, as the amino acid sequence homology showed a 97-98% to these strains. The Chinju99 had a very close relationship to the Japanese strain JMe2 for the nucleotide and amino acid sequences of the M gene. The amino acids predicted from Chinju99 M gene consisted of mostly hydrophobic residues and contained three potential sites for asparagine (N)-linked glycosylation, two serine (S)-linked phosphorylation sites by protein kinase C, and two S- or threonine (T)-linked phosphorylation sites by casein kinase II.

• Korean Journal of Veterinary Research
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• v.47 no.2
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• pp.169-174
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• 2007

To provide information for the molecular pathogenesis and antigenic structures of Korean isolates of porcine epidemic diarrhea virus (PEDV), the small membrane (sM) protein gene of Chinju99 strain, which was previously isolated from piglets suffering from severe diarrhea was characterized and further analyzed with other PEDV strains. The sM gene of Chinju99 generated by reverse transcription and polymerase chain reaction had a single open reading frame with 231 bases consisting of 24.2% adenine, 18.6% cytosine, 18.1% guanine and 39.0% thymine nucleotides. Nucleotide sequence of the gene revealed 97.8% homology to those of Belgian strain CV777 and British strain Br1/87, and 97.0% to Chinese strain LZC. The gene encoded a protein with 76 amino acids, and putative amino acid sequence of the gene revealed 98.7% homology to those of CV777 and Br1/87, and 96.1% to LZC. The amino acids of Chinju99 sM gene consisted of mostly hydrophobic residues, and there were one potential N-myristylation site and one potential threonine (T)-linked phosphorylation site recognized. Also, there was a transmembrane region with 46 amino acids, and Chinju99 was more close to CV777 and Br1/87 than to LZC in phylogenetic analysis on the sM amino acid sequences.

• YAKHAK HOEJI
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• v.55 no.1
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• pp.75-79
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• 2011

The replication competent adenoviral vector (AV), AdLPCDIRESE1A was generated and reported previously to have cytotoxic effects in some cell lines. In AdLPCDIRESE1A, the expression of cytosine deaminse (CD) and E1A genes are under the control of tumor-specific L-plastin promoter. CD enzyme can deaminate the nontoxic prodrug 5-fluorocytosine (5-FC) to the toxic 5-fluorouracil (5-FU). E1A gene is essential for viral replication. Primary liver cancer, most of which is hepatocellular carcinoma (HCC), is the third common leading cancer in Korea. Thus, we have conducted in vitro preclinical study to evaluate effectiveness of AdLPCDIRESE1A on HCC. The efficacy of cytotoxicity was measured by generation of cytopathic effect (CPE) and cell counting. We infected HepG2 cells with various MOI of vector alone or concurrent with 5-FC. Exposure of cells to AdLPCDIRESE1A generated a significant cytotoxic effect as compared to the control. Almost 83% of the cell had manifested the characteristic cytotoxic effect on day 9 after infection of cells with 10 MOI of vector. We also observed the additive cytotoxic effects when AdLPCDIRESE1A vector had been coadministrated with 5-FC. The results suggest that the use of AdLPCDIRESE1A/5FC may be value in treatment of liver cancer. Further animal studies are needed for clinical trial.

• Korean Journal of Plant Resources
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• v.20 no.6
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• pp.491-498
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• 2007

It has been hypothesized that efficient exclusion of methylated retrotransposons and repeated DNA region is one of the rapid and cost-effective approaches for comprehensive gene discovery in large genome size of maize. Three kinds of methylation-sensitive restriction enzymes, HapII, MspI and McrBC, were used to identify the restriction frequency of cytosine methylation sites in maize genome. Roughly 60% of total maize genomic DNA was restricted less than 500bp by McrBC, and the most of restricted small size fraction was composed retrotransposon. In order to validate the efficient construction of gene-rich shotgun library, we compare two gene-rich methyl-filtration shotgun libraries using in vivo and in vitro methyl-filtration system. The size selected DNA fraction by Sau3A-McrBC enzyme treated was very stable and has not appeared modification in E. coli, but most insert DNA size of partially digested with Sau3A were decrease less than 500bp by bacterial methylation-modification system. In compare of retroelements portion, A 44.6% of the sequences were retroelement in unmethyl-filtered library, and the most of them was Copia type, such as Prem, Opie and Ji. The portion of retroelement was drastically decreased to 25% and 20% by in vivo and in vitro filtration system, respectively.

• Archives of Pharmacal Research
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• v.19 no.3
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• pp.191-196
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• 1996

Bizelesin is a promising novel anticancer agent which is known to alkylate N3 of adenine to induce DNA interstrand cross-links (ISC) with in $5^I-TAATTA\; and\; 5^I-TAAAAAA$. We have investigated the base specificity for DNA ISC induced by bizelesin using oligomers containing the cross-linkable sequence $5^I-TAATTA\; and\; 5^I-TAAAAAA$. in which "N" was either A, C, G, or T. An analysis of denaturing polyacrylamide gel showed that bizelesin is able to induce DNA ISC in the duplex oligomer containing sequences $5^I-TAATTA\; and\; 5^I-TAAAAAA$. The formation of interstrand crosslinking did not occur in the sequences $5^I-TAATTA\; and\; 5^I-TAAAAAA$. DNA strand cleavage assay to determine the cross-linking site within $5^I-TAATTA$sequence showed that bizelesin alkylates guanine. These results demonstrate that bizelesin is able to induce DNA ISC at guanine but not at cytosine or thymine. In addition, guanine adducts have been found to be susceptible to DNA strand cleavage by exposure to hot piperidine. The extent of DNA strand cleavage, however, was not 100% efficient in either neutral pH buffer or hot piperidine.

• Korean Journal of Microbiology
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• v.29 no.4
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• pp.250-257
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• 1991

An obligate methanol-oxidizing bacterium, Methylobacillus sp. strain SK1, which grows only on methanol was isolated from soil. The isolate was nonmotile Gram-negtive rod. It does not have internal membrane system. The colonies were small, whitish-yellow, and smooth. The guanine plus cytosine content of the DNA was 48 mol%. Cellular fatty acids consisted predominantly of large amounts of straight-chain saturated $C_{16:0}$ acid and unsaturated $C_{16:1}$ acid. The major ubiquinone was Q-8, and Q-10 was present as minor component. The cell was obligately aerobic and exhibited catalase, but no oxidase, activity. Poly-.betha.-hydroxybutyrate, endospores, or cysts were not observed. the isolate could grow only on methanol in mineral medium. Growth factors were not required. The isolate was unable to use methane, formaldehyde, formate, methylamine, and several other organic compounds tested as a sole source of carbon and energy. Growth was optimal at 35.deg.C and pH 7.5. It could not grow at 42.deg.C. The doubling time was 1.2h at 30.deg.C when grown with 1.0%(v/v) methanol. The growth was not affected by antibiotics inhibiting cell wall synthesis and carbon monoxide but was completely suppressed by those inhibiting protein synthesis. Methanol was found to be assimilated through the ribulose monophosphate pathway. Cytochromes of b-, c-, and o- types were found. Cell-free extracts contained a phenazine methosulfate-linked methanol dehydrogenase activity, which required ammonium ions as an activator. Cells harvested after the late exponential phase seemed to contain blue protein.ein.

• Journal of Yeungnam Medical Science
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• v.23 no.1
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• pp.118-123
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• 2006

Dentatorubropallidoluysian atrophy (DRPLA) is a rare neurodegenerative disorder usually inherited in an autosomal dominant pattern. DRPLA has been shown to be associated with expansion of an unstable cytosine-adenine-guanine (CAG) trinucleotide repeat in a gene on chromosome 12p. We evaluated a family with DRPLA that affected three members; A 35-year-old female presented with seven year history of gait ataxia, dysarthria and mild cognitive impairment. The MRI of the brain revealed diffuse cerebellar atrophy with an incidental lipoma in the midbrain. Her 30-year-old brother presented with progressive cerebellar ataxia that developed at the age of 20. Her grandmother and mother were reported to have developed ataxia during the late period of their life, and died at the age of 60 and 55, respectively. The demonstration of an expanded CAG repeat in the gene for DRPLA was used to confirm the diagnosis.

• Journal of Veterinary Clinics
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• v.36 no.6
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• pp.353-357
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• 2019

A two-year-old spayed female Persian cat demonstrated weight loss, anorexia, and vomiting for one week. Hematologic findings suggested chronic renal failure. Radiography and ultrasonography revealed severe bilateral renomegaly with hypoechoic nodules and subcapsular hypoechoic rim. Fine needle aspiration of the kidney revealed malignant lymphoma. The cat received in-hospital treatment for chronic renal failure for seven days, followed by chemotherapy (cyclophosphamide, vincristine, and prednisolone). The cat tolerated chemotherapy well and chronic kidney disease was alleviated. However, complete remission was not achieved. After 93 days of treatment, the cat exhibited anisocoria and mental dullness. Brain magnetic resonance imaging revealed hypertrophy and enhancement of cranial nerves. Chemotherapy was replaced with lomustine (10 mg orally), and two weeks later, cytosine arabinoside (50 mg/㎡ subcutaneously), twice daily for consecutive days. Five days after substitution chemotherapy, the patient showed anemia due to severe intestinal bleeding and died. Post-mortem examination and histopathologic analysis confirmed renal T-cell lymphoma with metastasis to the central nervous system, colon, and nasal cavity. Survival time was 117 days after the diagnosis of renal lymphoma.