• Journal of Microbiology and Biotechnology
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• v.29 no.11
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• pp.1790-1798
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• 2019

Flock House virus (FHV), an insect RNA virus, has a bipartite genome. FHV RNA1 can be packaged in turnip yellow mosaic virus (TYMV) as long as the FHV RNA has a TYMV sequence at the 3'-end. The encapsidated FHV RNA1 has four additional nucleotides at the 5'-end. We investigated whether the recombinant FHV RNA1 could replicate in mammalian cells. To address this issue, we prepared in vitro transcribed FHV RNAs that mimicked the recombinant FHV RNA1, and introduced them into baby hamster kidney (BHK) cells. The result showed that the recombinant FHV RNA1 was capable of replication. An eGFP gene inserted into the frame with B2 gene of the FHV RNA1 was also successfully expressed. We also observed that eGFP expression at the protein level was strong at 28℃ but weak at 30℃. Sequence analysis showed that the 3'-ends of the RNA1 and RNA3 replication products were identical to those of the authentic FHV RNAs. This indicates that FHV replicase correctly recognized an internally-located replication signal. In contrast, the 5'-ends of recombinant FHV RNA1 frequently had deletions, indicating random initiation of (+)-strand synthesis.

• Proceedings of the Korean Information Science Society Conference
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• 2005.11b
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• pp.265-267
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• 2005

최근 포유동물의 유전체에는 알려진 것보다 훨씬 많은 RNA 전사체가 발현되고 있음이 밝혀지고 있으며, 그 중에 많은 부분이 non-coding RNA로 알려지고 있다. 세포 내에서 non-coding RNA의 기능이 훨씬 다양해지고, 중요해지고 있는 상황에서 새로운 non-coding RNA를 정의하고, 탐색하는 것은 가장 시급한 과제이다. 본 연구에서는 이전 연구에서 RNA 공통 구조 학습을 위해 제안되었던, esRCSG (evolutionary search for RNA common-structural grammar) 알고리즘의 성능 향상을 위해, committee machine을 도입한다. Committee machine은 마지막 세대에서 최적화된 RNA 공통 구조 기술자 (RCSD)와 차상위로 최적화된 기술자들 중 양성데이터와 음성데이터의 치역을 합쳤을 때 특이도는 거의 변화가 없으면서 민감도의 증가가 가장 큰 기술자들의 집합이다. Committee machine은 특히 family type의 서열의 가진 특정 ncRNA에서 좋은 성능 향상을 보인다. microRNA를 이용한 성능평가에서 특이도의 변화가 거의 없이 민감도의 성능이 약 1.5배 향상되는 결과를 보였다. 이러한 특이도와 민감도가 높은 기술자를 이용함으로써 새로운 non-coding RNA를 예측하는 것을 약속할 수 있을 것이다.

• Genomics & Informatics
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• v.17 no.1
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• pp.10.1-10.3
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• 2019

To identify miRNA-mRNA interaction pairs associated with binary phenotypes, we propose a hierarchical structural component model for miRNA-mRNA integration (HisCoM-mimi). Information on known mRNA targets provided by TargetScan is used to perform HisCoM-mimi. However, multiple databases can be used to find miRNA-mRNA signatures with known biological information through different algorithms. To take these additional databases into account, we present our advanced application software for HisCoM-mimi for binary phenotypes. The proposed HisCoM-mimi supports both TargetScan and miRTarBase, which provides manually-verified information initially gathered by text-mining the literature. By integrating information from miRTarBase into HisCoM-mimi, a broad range of target information derived from the research literature can be analyzed. Another improvement of the new HisCoM-mimi approach is the inclusion of updated algorithms to provide the lasso and elastic-net penalties for users who want to fit a model with a smaller number of selected miRNAs and mRNAs. We expect that our HisCoM-mimi software will make advanced methods accessible to researchers who want to identify miRNA-mRNA interaction pairs related with binary phenotypes.

• Korean Journal of Microbiology
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• v.27 no.1
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• pp.1-9
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• 1989

The locations of 5' ends as well as the splicing pattern of viral poly A(-) 19S RNA from monkey cells infected with SV40 were determined by a modification of primer extension method. The 5' end of this RNA mapped at the major cap site at nucleotide residue 325, used most frequently by SV40 late RNAs. The intron from nt.373 to nt.558 was removed as the ordinary cytoplasmic poly A(+) 19S RNA. The 3'end of this RNA was very heterogeneous and distributed over 1 kb upstream of polyadenylation site, as determined by S1 nuclease mapping. The reason for this normally initiated and spliced RNA to accumulate in the nucleus was investigated. In order to test whether the presence of unused 3' splice region on this RNA caused such subcellular distribution, cells were transfected with SV40 mutant KNA containing deletion around 3' splice site. The RNA deleted of 3' splice region accumulated mainly in the cytoplasm. This accumulation did not result from the increased stability of the RNA due to the deletion, since the wild type and mutant RNAs exhibited similar half lives after chase with actinomycin D. Therefore it is likely that the 19S spliced RNA is hindered from being transported into the cytoplasm due to some pre-splicing complexes formed at the unused 3' splice site.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.12
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• pp.4773-4780
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• 2014

Background: To investigate the effects of small interference RNA (siRNA) targeting BCR/ABL mRNA on proliferation and apoptosis in the K562 human chronic myeloid leukemia (CML) cell line and to provide a theoretical rationale and experimental evidence for its potential clinical application for anti-CML treatment. Materials and Methods: The gene sequence for BCR/ABL mRNA was found from the GeneBank. The target gene site on the BCR/ABL mRNA were selected according to Max-Planck-Institute (MPI) and rational siRNA design rules, the secondary structure of the candidate targeted mRNA was predicted, the relevant thermodynamic parameters were analyzed, and the targeted gene sequences were compared with BLAST to eliminate any sequences with significant homology. Inhibition of proliferation was evaluated by MTT assay and colony-formation inhibiting test. Apoptosis was determined by flow cytometry (FCM) and the morphology of apoptotic cells was identified by Giemsa-Wright staining. Western blotting was used to analyze the expression of BCR/ABL fusion protein in K562 cells after siRNA treatment. Results: The mRNA local secondary structure calculated by RNA structure software, and the optimal design of specific siRNA were contributed by bioinformatics rules. Five sequences of BCR/ABL siRNAs were designed and synthesized in vitro. Three sequences, siRNA1384, siRNA1276 and siRNA1786, which showed the most effective inhibition of K562 cell growth, were identified among the five candidate siRNAs, with a cell proliferative inhibitory rate nearly 50% after exposure to 12.5nmol/L~50nmol/L siRNA1384 for 24,48 and 72 hours. The 50% inhibitory concentrations ($IC_{50}$) of siRNA1384, siRNA1276 and siRNA1786 for 24hours were 46.6 nmol/L, 59.3 nmol/L and 62.6 nmol/L, respectively, and 65.668 nmol/L, 76.6 nmol/L, 74.4 nmol/L for 72 hours. The colony-formation inhibiting test also indicated that, compared with control, cell growth of siRNA treated group was inhibited. FCM results showed that the rate of cell apoptosis increased 24 hours after transfecting siRNA. The results of annexinV/PI staining indicated that the rate of apoptosis imcreased (1.53%, 15.3%, 64.5%, 57.5% and 21.5%) following treamtne with siRNAs (siRNA34, siRNA372, siRNA1384, siRNA1276 and siRNA1786). Morphological analysis showed td typical morphologic changes of apoptosis such as shrunken, fragmentation nucleus as well as "apoptotic bodies" after K562 cell exposure to siRNA. Western blot analysis showed that BCR/ABL protein was reduced sharply after a single dose of 50nmol/L siRNA transfection. Conclusions: Proliferation of K562 cells was remarkbly inhibited by siRNAs (siRNA1384, siRNA1276 and siRNA1786) in a concentration-dependent manner in vitro, with effective induction of apoptosis at a concentration of 50 nmol/L. One anti-leukemia mechanism in K562 cells appeared that BCR/ABL targeted protein was highly down-regulated. The siRNAs (siRNA1384, siRNA1276 and siRNA1786) may prove valuable in the treatment of CML.

• Korean Journal of Microbiology
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• v.24 no.2
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• pp.79-85
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• 1986

We have determined the sequence of $tRNA^{Arg}$ of A. nidulans partially by enzymatic rapid RNA sequencing technique. The sequence was 5'GGCCGGCUGGCCCAAXUGGCAAGGXUCUGAXUACGAAXCAGGAGAUUGCACXXXXXGAGCXXUXXGUCGGUCACCA3' The cloverleaf structure was made from above data. As a result, the anticodon sequence was identified as ACG. This result was confirmed with charging test. The complete sequence was proposed by supplementing the DNA sequence to and by assigning the position of minor bases to this RNA sequence.

• Korean Journal of Microbiology
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• v.30 no.3
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• pp.177-180
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• 1992

Among 120 U. maydis strains isolated in Korea 14 different strains containing specific viral dsRNA segments were analyzed for the distribution of dsRNA and the production of toxin protein. Several distinctive dsRNA patterns were identified, 9 cases of P type with typical H, M and L ds RNA and one case of non-P-type, the frequency of a specific isolate was decreased with increasing number of dsRNA segments. The presence of dsRNA had no effect on the cultural or morphological phenotype of the host. Two isolates containing P type dsRNA segments appeared to produce toxin protein (killer strains) which inhibited the growth of 4 isolates (sensitive strain) with different susceptibility. Two killer strains contain unique M dsRNA segment which may code for toxin protein. However, the presence of toxin-sensitive strains among dsRNA-free isolates was similar to that of ds RNA containing strains.

• Molecules and Cells
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• v.39 no.3
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• pp.179-185
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• 2016

Posttranscriptional regulation of RNA metabolism, including RNA processing, intron splicing, editing, RNA export, and decay, is increasingly regarded as an essential step for fine-tuning the regulation of gene expression in eukaryotes. RNA-binding proteins (RBPs) are central regulatory factors controlling posttranscriptional RNA metabolism during plant growth, development, and stress responses. Although functional roles of diverse RBPs in living organisms have been determined during the last decades, our understanding of the functional roles of RBPs in plants is lagging far behind our understanding of those in other organisms, including animals, bacteria, and viruses. However, recent functional analysis of multiple RBP family members involved in plant RNA metabolism and elucidation of the mechanistic roles of RBPs shed light on the cellular roles of diverse RBPs in growth, development, and stress responses of plants. In this review, we will discuss recent studies demonstrating the emerging roles of multiple RBP family members that play essential roles in RNA metabolism during plant growth, development, and stress responses.

• Korean Journal of Microbiology
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• v.26 no.2
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• pp.106-112
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• 1988

We have examined the structures and cellular distributions of the SV40 late RNAs present in monkey cells at late times after infection. One particular RNA species, spliced at residue 373(373-RNA), was found to be as abundant as the major late 16S RNAs. This result was unexpected since previous reports showed that the molecular ratio of the 373-spliced 19S RNA to 16S RNA is approximately 0.1 among either cytoplasmic polyadenylated or polysomal viral RNAs. Both sedimentation and electrophoretic analysis indicated that the 373-RNA was approximately 16S to 19S in size. Therefore, it was not a splicing intermediate or the product of premature termination of transcription within the late leader region. Whereas most SV40 late 16S RNA is polyadenylated and located in the cytoplasm, the majority of 373-RNA was found to lack poly A, and be located in the nucleus.

• Journal of radiological science and technology
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• v.21 no.1
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• pp.65-68
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• 1998

We attempted to purify radiolabeled RNA using Sephadex G-15 and G-50 chromatography instead of commercial RNA purification kit. In the Sephadex G-15 chromatography the major portion of RNA was eluted in the fractions ranging from 3rd to 5th whereas broad elution profile of RNA was obtained from the Sephadex G-50 chromatography. The elution profile and purity of RNA obtained from Sephadex G-15 chromatography was very similar to that by commercial RNA purification kit. Furthermore, operating time required for purification of RNA by Sephadex G-15 was rather smaller than that by commercial kit. Overall results suggest that the purification of radiolabeled RNA using Sephadex G-15 is more money and time saying than using commercial RNA purification kit.