• Asian Pacific Journal of Cancer Prevention
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• v.15 no.23
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• pp.10513-10524
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• 2015

Background: Metastasis is a major reason for poor prognosis in patients with cancer, including hepatocellular carcinoma (HCC). A salient feature is the ability of cancer cells to colonize different organs. Long non-coding RNAs (lncRNAs) play important roles in numerous cellular processes, including metastasis. Materials and Methods: In this study, the lncRNA expression profiles of two HCC cell lines, one with high potential for metastasis to the lung (HCCLM3) and the other to lymph nodes (HCCLYM-H2) were assessed using the Arraystar Human LncRNA Array v2.0, which contains 33,045 lncRNAs and 30,215 mRNAs. Coding-non-coding gene co-expression (CNC) networks were constructed and gene set enrichment analysis (GSEA) was performed to identify lncRNAs with potential functions in organ-specific metastasis. Levels of two representative lncRNAs and one representative mRNA, RP5-1014O16.1, lincRNA-TSPAN8 and TSPAN8, were further detected in HCC cell lines with differing metastasis potential by qRT-PCR. Results: Using microarray data, we identified 1,482 lncRNAs and 1,629 mRNAs that were differentially expressed (${\geq}1.5$ fold-change) between the two HCC cell lines. The most upregulated lncRNAs in H2 were RP11-672F9.1, RP5-1014O16.1, and RP11-501G6.1, while the most downregulated ones were lincRNA-TSPAN8, lincRNA-CALCA, C14orf132, NCRNA00173, and CR613944. The most upregulated mRNAs in H2 were C15orf48, PSG2, and PSG8, while the most downregulated ones were CALCB, CD81, CD24, TSPAN8, and SOST. Among them, lincRNA-TSPAN8 and TSPAN8 were found highly expressed in high lung metastatic potential HCC cells, while lowly expressed in no or low lung metastatic potential HCC cells. RP5-1014O16.1 was highly expressed in high lymphatic metastatic potential HCC cell lines, while lowly expressed in no lymphatic metastatic potential HCC cell lines. Conclusions: We provide the first detailed description of lncRNA expression profiles related to organ-specific metastasis in HCC. We demonstrated that a large number of lncRNAs may play important roles in driving HCC cells to metastasize to different sites; these lncRNAs may provide novel molecular biomarkers and offer a new basis for combating metastasis in HCC cases.

• The Microorganisms and Industry
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• v.13 no.1
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• pp.4-9
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• 1987

The regulation of gene expression in procaryotes is accomplished primarily at the level of transcription. Initiation of transcription is subject to numerous promoter-specific controls which act to ensure coordinate expression of disparate genes. The kinetics of formation of a functional("open") complex at a promoter, prior to the catalytic steps of RNA chain initiation and elongation, is thought to play a major role in controlling the efficiency of transcription of that promotor, since the subsequent processes of nucleotide binding and phosphodiester bond formation are rapid and are not promoter-specific (Mangel and Chamberlin, 1974 Shimamoto et al., 1981)

• Korean Journal of Environmental Biology
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• v.22 no.2
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• pp.329-335
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• 2004

To develop a biomarker for the monitoring of the contamination of estrogenic endocrine disrupters in the aquatic environment, reverse transcription -polymerase chain reaction (RT-PCR) analysis of vitellogenin (Vg) mRNA expression was optimized in Bombina orientalis, a Korean red bellied toad species. Based on partial cDNA sequences of both Vg and beta actin genes of B. orientalis, specific primers for RT-PCR of Vg and beta actin mRNAs were developed. Semiquantitative RT-PCR of the Vg mRNA in liver was optimized using a beta actin mRNA as an internal control in both sexes. In female RT-PCR using $1\;\mu{g}$ of the liver cDNA resulted in a linear increment in the PCR product of Vg from 18 to 34 cycles of amplification. In male, on the contrary, the RT- PCR product was first detected at 30 cycles of amplification and a linear increment was observed from 30 to 40 cycles of amplification, suggesting that male B. orientalis expresses minute amount of Vg mRNA which is a $2^{-12}$ equivalent of female. In conclusion, the optimized protocol for semiquantitative RT-PCR analysis of Vg mRNA level in B. orientalis male liver will be useful for the environmental monitoring the xenoestrogen contamination in the freshwater environment in Korea.

• The korean journal of orthodontics
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• v.34 no.2 s.103
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• pp.143-152
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• 2004

It has not been elucidated whether the initiation of condylar development of the mandible is related with the periosteum of the mandible, or if it derives from a separate programmed blastema not related with the mandible. Also, although the mandibular condylar cartilage is known to promote growth, few studies have dealt with molecular-biologic mechanisms such as the expression of specific genes according to the differentiation of the mandibular condyle. To elucidate the unique cellular characteristics, development, and differentiation process of the mandibular condyle, an examination of expressions of genes characteristic of cartilage and bone were carried out using RT-PCR and mRNA in situ hybridization. 1. Type? collagen mRNA was detected with type II collagen mRNA in the differentiation and growth process of the cartilage of the mandibular condyle. TypeII collagen mRNA was demonstrated in the whole resting md upper part of the poliferative zone, whereas type II collagen mRNA was observed in the resting, proliferative and upper hypertrophic cartilage zone of the mandibular condyle. 2. The condylar cartilage rapidly increased in size due to the accumulation of hypertrophic chondrocytes as characterized by the expression of type II collagen mRNA during postnatal development. 3. BMP-4 mRNA was present in the anlage of the future condylar process and also in the ossifying mandibular body. 4. IHH mRNA was limited exclusively to the lower part of the proliferative zone and the upper part of the hypertrophic cartilage zone during condylar development. These findings were different from those in the growth-plate cartilage of the long bone, indicating a characteristic feature of the differentiation of the chondrocytes in the condylar cartilage present in prenatal and postnatal development. Furthermore, it was also suggested that chondroblasts of condylar cartilage rapidly differentiate into hypertrophic chondrocytes with increased functional Load force such as muscle activity and mastication.

• Bulletin of the Korean Chemical Society
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• v.28 no.6
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• pp.1010-1014
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• 2007

M1 RNA is the catalytic component of RNase P, a tRNA-processing enzyme in Escherichia coli. M1 RNA is produced in the cell by transcription of the rnpB gene and subsequent processing at the 3' end. The 3' flanking region of rnpB contains repeated sets of overlapping sequences coding for small proteins. The issue of whether these proteins are expressed remains to be established. In this study, we showed the expression of a small protein encoded by the first repeat within the 3' flanking region of rnpB. Interestingly, protein expression was increased at lower temperatures. The termination efficiency of rnpB terminators was decreased at lower temperatures, suggesting that antitermination is responsible for enhanced protein expression. Moreover, the purified small protein contained M1 RNA, implying a role as a specific RNA-binding protein.

• Proceedings of the Korea Information Processing Society Conference
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• 2014.04a
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• pp.671-674
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• 2014

최근 MicroRNA(miRNA)가 질병 발생과 밀접한 연관성이 있다고 밝혀진 이래, 이와 관련된 연구가 활발히 진행되고 있다. 하지만 각종 질병 관련 miRNA의 기능과 역할 그리고 질병 발생 메카니즘 등이 명백히 밝혀진 것이 없는 실정이다. 본 논문에서는 여러 종류의 miRNA 데이터베이스(miRecords, miRTarBase, miR2Disease 등)를 통합하고, 본 논문에서 새로이 제안하는 scoring 방법과 특정 질병과 관련된 miRNA의 순위결정과정을 통하여 질병과 연관성이 높은 miRNA을 밝혀내는 방법을 제안한다. 새로이 제안하는 방법을 바탕으로 miRNA와 특정 질병과의 연관성을 효과적으로 밝혀냈다.

• Journal of Microbiology
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• v.37 no.4
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• pp.243-247
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• 1999

Effects of divalent cations on self-splicing inhibition by the antibiotic spectinomycin of the phage T4 thymidylate synthase intron (td) have been investigated. $Ca^{2+}$ ion at 1mM concentration suppressed splicing inhibition of spectinomycin by 10% and 50 ${\mu}M\;Co^{2+}$ ion also suppressed splicing inhibition of specinomycin by 10%. $Mg^{2+}$ ion at 6 mM concentration decreased splicing inhibition of spectinomycin by 42% while $Mn^{2+}$ ion decreased the splicing inhibition by 10%. $Zn^{2+}$ ion at 10 uM concentration lowered the splicing inhibition by spectinomycin of 15%. Of all divalent cations tested, $Mg^{2+}$ ion was the most effective in suppressing splicing inhibition by specinomycin whereas $Ca^{2+}$ ion was the least effective. The results suggest that spectinomycin may interact with specific and functional $Mg^{2+}$-binding sites within intron RNA that lead to a displacement of $Mg^{2+}$ essential for catalytic activity.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.878-884
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• 2013

Salmonella is a major foodborne pathogen that causes a variety of human diseases. Development of ligands directly and specifically binding to the Salmonella will be crucial for the rapid detection of, and thus for efficient protection from, the virulent bacteria. In this study, we identified a RNA aptamer-based ligand that can specifically recognize Salmonella Typhimurium through SELEX technology. To this end, we isolated and characterized an RNase-resistant RNA aptamer that bound to the OmpC protein of Salmonella Typhimurium with high specificity and affinity ($K_d$ ~ 20 nM). Of note, the selected aptamer was found to specifically bind to Salmonella Typhimurium, but neither to Gram-positive bacteria (Staphylococcus aureus) nor to other Gram-negative bacteria (Escherichia coli O157:H7). This was evinced by aptamer-immobilized ELISA and aptamer-linked precipitation experiments. This Salmonella species-specific aptamer could be useful as a diagnostic ligand against pathogen-caused foodborne sickness.

• Journal of Photoscience
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• v.7 no.2
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• pp.73-78
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• 2000

To analyze molecular traits determining pigmentation between Pharbitis nill violet and white, Amplified Fragment Length Polymorphism(AFLP) and Differential Display Reverse Transcription(DDRT) experiments were carried out with either genomic DNAs or total RNAs isolated from both plants. Results of AFLP experiment in combination of 8 EcoRⅠ primers with 6 MseⅠ primers showed 41 violet-and 60 white-specific DNA bands. In the subsequent experiment, 22 violet-and 22 white-specific DNA fragments were amplified by PCR with DNAs eluted. The sizes of the fragments range from 200 to 600bp. DDRT using total RNA produced 19 violet-and 17 white-specific cDNA fragments, ranging from 200 to 600bp. The fragments obtained by both AFLP and DDRT had been cloned into pGEM T-easy vector, amplified and subjected to the nucleotide sequence analyses. As a result of Blast sequence analysis, most of them sequenced up to date showed no similarity to any Known gene, while few has similarity to known animal or plant genes. An AFLP clone V6, for example, has a strong sequence similarity to the human transcription factor LZIP-alpha mRNA and a DDRT clone W19 to Solanum tuberosum 3-hydroxy-3-methylglutaryl coenzyme A reductase mRNA.

• Applied Biological Chemistry
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• v.32 no.3
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• pp.222-231
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• 1989

Three classes of proteinase inhibitors are known in soybean; the Kunitz trypsin inhibitor (SKTI), the Bowman-Birk proteinase inhibitor and its isoinhibitors. To study the molecular structure and expression characteristics of the SKTI, antibody was obtained by immunizing rabbit with the SKTI purified from soybean by preparative electrophoresis. Anti-SKTI antibody was not only specific for mature SKTI in soybean seed but also recognized the precursor which was synthesized in vitro. Translation in vitro was carried out in wheat germ extract with polyadenylated mRNA isolated from developing soybean seeds. One of the seed specific translation products, MW 24K, was identified to be the precursor for the SKTI by immunoprecipitation with anti-SKTI antibody. Mature SKTI of MW 20K, however, was not detected in the translates in vitro. These results suggest that the precursor polypeptide is synthesized from the mRNA and is cleaved to yield mature SKTI in soybean seed. The SKTI gene was expressed with the maturation of soybean seed in a tissue-specific and development stage-specific manner.