• Genes and Genomics
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• v.40 no.11
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• pp.1213-1223
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• 2018

Pelagic larval dispersal habits influence the population genetic structure of marine mollusk organisms via gene flow. The genetic information of the clam Gomphina aequilatera (short larval stage, 10 days) which is ecologically and economically important in the China coast is unknown. To determine the influence of planktonic larval duration on the genetic structure of G. aequilatera. Mitochondrial markers, cytochrome oxidase subunit i (COI) and 12S ribosomal RNA (12S rRNA), were used to investigate the population structure of wild G. aequilatera specimens from four China Sea coastal locations (Zhoushan, Nanji Island, Zhangpu and Beihai). Partial COI (685 bp) and 12S rRNA (350 bp) sequences were determined. High level and significant $F_{ST}$ values were obtained among the different localities, based on either COI ($F_{ST}=0.100-0.444$, P<0.05) or 12S rRNA ($F_{ST}=0.193-0.742$, P<0.05), indicating a high degree of genetic differentiation among the populations. The pairwise $N_m$ between Beihai and Zhoushan for COI was 0.626 and the other four pairwise $N_m$ values were >1, indicating extensive gene flow among them. The 12S rRNA showed the same pattern. AMOVA test results for COI and 12S rRNA indicated major genetic variation within the populations: 77.96% within and 22.04% among the populations for COI, 55.73% within and 44.27% among the populations for 12S rRNA. A median-joining network suggested obvious genetic differentiation between the Zhoushan and Beihai populations. This study revealed the extant population genetic structure of G. aequilatera and showed a strong population structure in a species with a short planktonic larval stage.

• Bulletin of the Korean Chemical Society
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• v.26 no.12
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• pp.2033-2037
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• 2005

In vitro selection was used to isolate $Mg^{2+}$-dependent self-cleaving ribozymes with cis-cleavage activity from a pre-tRNA library having 40-mer random sequences attached to 5'-end of E. coli $tRNA^{Phe}$. After 8 rounds of SELEX (Systematic Evolution of Ligands by Exponential Enrichment), RNA molecules which can self-cleave at the high concentration of $Mg^{2+}$ were isolated. The selected ribozymes can carry out the self-cleavage reaction in the presence of 100 mM $Mg^{2+}$ but not in 10 mM $Mg^{2+}$. The cleavage sites of the ribozymes are located at +3 and +4 of $tRNA^{Phe}$, compared with +1 position of 5'-end cleavage site of pre-tRNA by RNase P. New RNA constructs deprived of its D stem-loop, anticodon stem-loop, variable loop and T stem-loop, respectively showed the cleavage specificity identical to a ribozyme having the intact tRNA structure. Also, the new ribozyme fused with both a ribozyme and $tRNA^{Leu}$ showed the cleavage activities at the various sites within its sequences, different from two sites of position +3 and +4 observed in the ribozyme with $tRNA^{Phe}$. Our results suggest that the selected ribozyme is not structural-specific for tRNA.

• Korean Journal of Microbiology
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• v.25 no.2
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• pp.94-102
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• 1987

Rat liver LDH A-cDNA has been isolated from a .lambda.gt11-rat lover cDNA library and partially characterized. The size of the isolated rat liver LDH A-cDNA if shown to be 1.6Kb and restriction enzyme sites for the rat liver LDH A-cDNA are also mapped. 682-nucleotide sequence coding for 3'-end of rat liver LDH A-cDNA has been analyzed and compared to the nucleotide sequence of the same region of rat $C_6$-glioma cell LDH A-cDNA which has been cloned from the hormonally stimulated cell cultures. The result shows that 177 nucleotide sequences coding for the C-terminal 59-amino acids are identical but 505 nucleotide sequences of 3'-nontranslated region of the two LSH A-cDNA exhibit characteristic differences in thier nucleotide sequences. Computer analysis for the folding structures for 3'-end 400 nucleotide sequences of the two LDH A-cDNA shows a possibility implying that the two LDH A-mRNAs isolated from different tissues of rats may have different half life and therefore their translational efficiency may be different. It has been previously demonstrated that isoproterenol stimulated rat $C_6$ -glioma cell cultures produce LDH A-mRNA showing 2 to 3-fold longer half life in comparison to that of noninduced LHD A-mRNA. The result therefore support for the idea that hormonally stimulated rat $C_6$-glioma cells may produce LDH A-mRNA containing different nucleotide sequences at the 3'-end nontranslated region by which the hormonally induced LDH A-mRNA could have more stable secondary mRAN structure in comparison to that of noninduced LDH A-mRNA.

• Journal of the Korean Chemical Society
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• v.38 no.10
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• pp.769-773
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• 1994

Higher order structure of 5S rRNA isolated from Xanthomonas celebensis was examined using angiogenic extracted from milk. Angiogenin cleaved exclusively 3' P-O bonds on the far sides of pyrimidines in the single-stranded sequences of 5S rRNA. Whereas angiogenin acted only on the loop d of 5S rRNA at pH 7.0 in the presence of 10 mM $Mg^{2+}$, it acted on all the loops (a, b, c and d) except loop e in the absence of $Mg^{2+}$. In the absence of $Mg^{2+}$, bonds $U_{74}$-$G_{75}$, $U_{77}$-$A_{78}$ and $U_{103}$-$A_{104}$ were highly susceptible to the action of angiogenin both at pH 7.0 and at pH 3.5. On the other hand, at pH 3.5 in the absence of $Mg^{2+}$ angiogenin strongly cleaved the bond $C_{17}$-$G_{18}$ of loop a and the bond $U_{55}$-$G_{56}$ of loop b. The results lead us to the following conclusion. First, angiogenin can be used as one of the probes for the tertiary structure analysis of 5S rRNA. Second, the structure of loop d of 5S rRNA is variable depending on the concentrations of $Mg^{2+}$ and $H^{1+}$.

• Communications of the Korean Mathematical Society
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• v.39 no.1
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• pp.223-245
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• 2024

We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots emphasize a biomolecule's entanglement while ignoring their intrachain interactions. We remedy this by using stuck knots and links, which provide a way to emphasize both their entanglement and intrachain interactions. We first give a generating set of the oriented stuck Reidemeister moves for oriented stuck links. We then introduce an algebraic structure to axiomatize the oriented stuck Reidemeister moves. Using this algebraic structure, we define a coloring counting invariant of stuck links and provide explicit computations of the invariant. Lastly, we compute the counting invariant for arc diagrams of RNA foldings through the use of stuck link diagrams.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.2
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• pp.50-55
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• 2016

Backbone $^1H$, $^{13}C$ and $^{15}N$ resonance assignments are presented for the anticodon binding domain (residues 557-674) of human glycyl-tRNA synthetase (GRS). Role of the anticodon binding domain (ABD) of GRS as an anticancer ligand has recently been reported and its role in other diseases like Charcot-Marie-Tooth (CMT) and polymyositis have increased its interest. NMR assignments were completed using the isotope [$^{13}C/^{15}N$]-enriched protein and chemical shifts based secondary structure analysis with TALOS+ demonstrate similar secondary structure as reported in X-ray structure PDB 2ZT8, except some C-terminal residues. NMR signals from the N-terminal residues 557 to 571 and 590 to 614 showed very weak or no signals exhibiting dynamics or conformational exchange in NMR timescale.

• Korean Journal of Plant Resources
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• v.20 no.6
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• pp.511-517
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• 2007

A stable method for strain distinction using viral RNA 1 structures analyses was developed and compared with the combined RT-PCR and RAPD methods. Seven out of 61 random primers were found to be polymorphic based on RAPD analysis resulting on the differentiation of the 33 BaYMV isolates into four distinct groups according to geographical districts. The first and largest group includes 13 isolate and consists mainly of two-rowed malting barley in Haenam area. The second group had ten collections from inland in west southern. The third group had seven isolates from west southern coastal region, where mainly six-rowed naked barley is cultivated. The last fourth group included three isolates from Gyungnam region in east southern area. Conclusively, RNA 1 analysis proved to be stable and efficient method for strain distinction for Korean BaYMV isolates. Further, results of pathogenicity and RNA 1 structure analyses revealed four groups BaYMV strains and were distributed all over Korea, represented by Naju, Haenam-okcheon, Iksan and Milyang.

• Proceedings of the Zoological Society Korea Conference
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• 1998.04a
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• pp.37.1-37
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• 1998

No Abstract, See Full Text

• The Korean Journal of Physiology and Pharmacology
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• v.12 no.4
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• pp.143-148
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• 2008

Caveolin-1 (CAV1) is an integral membrane protein that may function as a scaffold for plasma membrane proteins and acts as a tumor suppressor protein. One causative factor of chemotherapy-resistant cancers is P-plycoprotein (P-gp), the product of the multidrug resistance-1 gene (MDR1), which is localized in the caveolar structure. Currently, the interactive roles of CAV1 and MDR1 expression in the death of cancer cells remain controversial. In this study, we investigated the effects of indomethacin on the cell viability and the expression levels of MDR1 mRNA and protein in a CAV1-siRNA-mediated gene knockdown hepatoma cell line (SK-Hep1). Cell viability was significantly decreased in CAV1-siRNA-transfected cells compared with that of control-siRNA-transfected cells. Furthermore, the viability of cells pretreated with CAV1 siRNA was markedly decreased by treatment with indomethacin (400${\mu}$M for 24 h). However, the protein and mRNA levels of MDR1 were unchanged in CAV1-siRNA-transfected cells. These results suggest that CAV1 plays an important role as a major survival enzyme in cancer cells, and indomethacin can sensitively induce cell death under conditions of reduced CAV1 expression, independent of MDR1 expression.

• Journal of Microbiology
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• v.33 no.2
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• pp.136-141
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• 1995

From a cluster of structural rRNA genes which has previsouly been cloned (Hwang and Kim, in submission; J. Microbiol. Biotechnol.), a 1.0-kb Eco RI fragment of DNA which shows significant homology to the 25S and rRNA s of Tricholoma matsutake was used for sequence analysis. Nucleotide sequence was bidirectionally determined using delection series of the DNA fragment. Comparing the resultant 1016-base sequence with sequences in the database, both the 3'end of 25S-rRNA gene and 5S rRNA gene were searched. The 5S rRNA gene is 118-bp in length and is located 158-bp downstream of 3'end of the 25S rRNA gene. IGSI and IGS2 (partial) sequences are also contained in the fragment. Multiple alignment of the 5S rRNA sequences was carried out with 5S rRNA sequences from some members of the subdivision Basidiomycotina obtained from the database. Polygenetic analysis with distance matrix established by Kimura's 2-parameter method and phylogenetic tree by UPGMA method proposed that T. matsutake is closely related to efibulobasidium allbescens. Secondary structure of 5S rRNA was also hypothesized to show similar topology with its generally accepted eukaryotic counterpart.