• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.77-85
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• 2004

A significant portion (about 8% in human genome) of mammalian mRNA sequences contains AU(Adenine and Uracil) rich elements or AREs at their 3' untranslated regions (UTR). These mRNA sequences are usually stable. ARE motifs are assorted into three classes. The importance of AREs in biology is that they make certain mRNA unstable. We analyzed the occurrences of AREs and Alu, and propose a possible mechanism on how human mRNA could acquire and keep A REs at its 3' UTR originated from Alu repeats. Interspersed in the human genome, Alu repeats occupy 5% of the 3' UTR of mRNA sequences. Alu has poly-adenine (poly-A) regions at the end that lead to poly -thymine (poly-T) regions at the end of its complementary Alu. It has been discovered that AREs are present at the poly -T regions. In the all ARE's classes, 27-40% of ARE repeats were found in the poly -T region of Alu with mismatch allowed within 10% of ARE's length from the 3' UTRs of the NCBI's reference m RNA sequence database. We report that Alu, which has been reported as a junk DNA element, is a source of AREs. We found that one third of AREs were derived from the poly -T regions of the complementary Alu.

• Childhood Kidney Diseases
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• v.12 no.1
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• pp.11-22
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• 2008

Telomeres consist of tandem guanine-thymine(G-T) repeats in most eukaryotic chromosomes. Human telomeres are predominantly linear, double stranded DNA as they ended in 30-200 nucleotides(bases,b) 3'-overhangs. In DNA replication, removal of the terminal RNA primer from the lagging strand results in a 3'-overhang of uncopied DNA. This is because of bidirectional DNA replication and specificity of unidirectional DNA polymerase. After the replication, parental and daughter DNA strands have unequal lengths due to a combination of the end-replication problem and end-processing events. The gradual chromosome shortening is observed in most somatic cells and eventually leads to cellular senescence. Telomere shortening could be a molecular clock that signals the replicative senescence. The shortening of telomeric ends of human chromosomes, leading to sudden growth arrest, triggers DNA instability as biological switches. In addition, telomere dysfunction may cause chronic allograft nephropathy or kidney cancers. The renal cell carcinoma(RCC) in women may be less aggressive and have less genomic instability than in man. Younger patients with telomere dysfunction are at a higher risk for RCC than older patients. Thus, telomeres maintain the integrity of the genome and are involved in cellular aging and cancer. By studying the telomeric DNA, we may characterize the genetic determinants in diseases and discover the tools in molecular medicine.

• 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.

• Journal of Crop Science and Biotechnology
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• v.10 no.4
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• pp.237-242
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• 2007

Genome duplication(i.e. polyploidy) is a common phenomenon in the evolution of plants. The objective of this study was to achieve a comprehensive understanding of genome duplication for SNP discovery by Thymine/Adenine(TA) cloning for confirmation. Primer pairs were designed from 793 EST contigs expressed in the roots of a supernodulating soybean mutant and screened between 'Pureunkong' and 'Jinpumkong 2' by direct sequencing. Almost 27% of the primer sets were failed to obtain sequence data due to multiple bands on agarose gel or poor quality sequence data from a single band. TA cloning was able to identify duplicate genes and the paralogous sequences were coincident with the nonspecific peaks in direct sequencing. Our study confirmed that heterogeneous products by the co-amplification of a gene family member were the main cause of obtaining multiple bands or poor quality sequence data in direct sequencing. Counts of amplified bands on agarose gel and peaks of sequencing trace suggested that almost 27% of nonrepetitive soybean sequences were present in as many as four copies with an average of 2.33 duplications per segment. Copy numbers would be underestimated because of the presence of long intron between primer binding sites or mutation on priming site. Also, the copy numbers were not accurately estimated due to deletion or tandem duplication in the entire soybean genome.

• Bulletin of the Korean Chemical Society
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• v.28 no.4
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• pp.601-606
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• 2007

The chromatographic behaviors of nucleotides (inosine 5'-monophosphate, uridine 5'-monophosphate, guanosine 5'-monophosphate, and thymine monophosphate disodium salts) on a C18 column were studied with different types of ionic liquids (ILs) as additives for the mobile phase in reversed-phase liquid chromatography (RPLC). Three ILs, 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF4]), 1-ethyl-3-methylimidazolium tetrafluoroborate ([EMIm][BF4]), and 1-ethyl-3-methylimidazolium methylsulfate ([EMIm][MS]), were used. Eluents were composed of water and methanol (90/10%, vol) with the addition of 0.5-13.0 mM of ILs. The effects of the concentration of ILs on retention and separation were investigated and discussed. The results showed that the addition of ILs affects the retention and resolution of the tested compounds. Use of 13.0 mM of [BMIm][BF4] as the eluent modifier resulted in a baseline separation of nucleotides without requiring gradient elution. This study demonstrates that ILs can be potentially applied as a mobile phase modifier in RPLC.

• 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.26 no.4
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• pp.368-374
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• 1988

Enzymological proprties of an extracellular cytosine deaminase from Bacellus polymyxa YL 38-3 were investigated. The extracellular enzyme was very stable, and optimum pH and temperature for the enzyme activity were found to be near pH 6.0 in 0.2M potassium phosphate buffer and at $30^{\circ}C$, respectively. 5-Fluorocytosine was converyed to 5-fluorouracil by the enzyme, but 5-methylcytosine was not to thymine by it. The enzyme activity was completely inhibited by some heavy metal ion such as 1mM of $Cd^{2-}$ and $Hg^{2+}$, and by 1mM of p-chloromercuribenzoate, respectively. The enzyme activity was inactivated about 75% by 1mM of o-phenanthroline and monoiodoacetate. But the enzyme activity was stimulated up to 200% by 1mM of 2-mercaptoethanol.

• Journal of Microbiology and Biotechnology
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• v.29 no.2
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• pp.268-273
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• 2019

The specificity of a Bacillus licheniformis uridine diphosphate (UDP) glycosyltransferase, YjiC, was increased towards thymidine diphosphate (TDP)-sugar by site-directed mutagenesis. The Arg-282 of YjiC was identified and investigated by substituting with Trp. Conversion rate and kinetic parameters were compared between YjiC and its variants with several acceptor substrates such as 7-hydroxyflavone (7-HF), 4',7-dihydroxyisoflavone, 7,8-dihydroxyflavone and curcumin. Molecular docking of TDP-glucose and 7-HF with YjiC model showed pi-alkyl interaction with Arg-282 and His-14, and pi-pi interaction with $His^{14}$ and thymine ring. YjiC (H14A) variant lost its glucosylation activity with TDP-glucose validating significance of His-14 in binding of TDP-sugars.

• Journal of Photoscience
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• v.9 no.2
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• pp.439-441
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• 2002

Cyanobacteria are the dominant micro flora in rice-fields, contributing significantly to fertility as a natural biofertilizer. Recent studies show a continuous depletion of the stratospheric ozone layer, and the consequent increase in solar UV-B (280-315 nm) radiation reaching the Earth's surface. UV-B radiation causes reduction in growth, survival, protein content, heterocyst frequency and fixation of carbon and nitrogen in many cyanobacteria. UV -B induced bleaching of pigments, disassembly of phycobilisomal complexes, thymine dimer formation and alterations in membrane permeability have also been encounterd in a number of cyanobacteria. However, certain cyanobacteria produce photoprotective compounds such as water soluble colorless mycosporine-like amino acids (MAAs) and the lipid soluble yellow-brown colored sheath pigment, scytonemin, to counteract the damaging effects of UV-B. Cyanobacteria, such as Anabaena sp., Nostoc commune, Scytonema sp. and Lyngbya sp. were isolated from rice fields and other habitats in India and screened for the presence of photoprotective compounds. A circadian induction of the synthesis of MAAs by UV -B was noted in a number of cyanobacteria. Polychromatic action spectra for the induction of MAAs in Anabaena sp. and Nostoc commune also show the induction to be UV-B dependent peaking at 290 nm. Another photoprotective compound, scytonemin, with an absorption maximum at 386 nm (also absorbs at 300, 278, 252 and 212 nm), was detected in many cyanobacteria. In conclusion, a particular cyanobacterium having photoprotective compounds may be a potent candidate as biofertilizer for crop plants.