• Journal of Microbiology
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• 제42권3호
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• pp.200-204
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• 2004

Retron is a prokaryotic genetic element that produces multicopy single-stranded DNA covalently linked to RNA (msDNA) by a reverse transcriptase. It was found that cells producing a large amount of msDNA, rather than those that did not, showed a higher rate of mutation. In order to understand the molecular mechanism connecting msDNA production to the high mutation rate the protein patterns were compared by two dimensional gel electrophoresis. Ten proteins were found to be differentially expressed at levels more than three fold greater in cells with than without msDNA, nine of which were identified by MALDI TOF MS. Eight of the nine identified proteins were repressed in msDNA-producing cells and, surprisingly, most were proteins functioning in the dissimilation of various carbon sources. One protein was induced four fold greater in the msDNA producing cells and was identified as a 30S ribosomal protein S2 involved in the regulation of translation. The molecular mechanism underlying the elevated mutation in msDNA-producing cell still remains elusive.

• Genomics & Informatics
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• 제14권1호
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• pp.29-33
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• 2016

A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences. Among 16,844 bacterial sequences possessing a retron-type RT domain, we identified 48 unique types of msDNA. Currently, the biological role of msDNA is not well understood. Our work will be a useful tool in studying the distribution, evolution, and physiological role of msDNA.

• Nutrition Research and Practice
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• 제7권4호
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• pp.281-286
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• 2013

We examined the effect of parental folate deficiency on the folate content, global DNA methylation, folate receptor-alpha (FR${\alpha}$), insulin-like-growth factor-2 (IGF-2) and -1 receptor (IGF-1R) in the liver and plasma homocysteine in the postnatal rat. Male and female rats were randomly fed a folic acid-deficient (paternal folate-deficient, PD and maternal folate-deficient, MD), or folic acid-supplemented diet (paternal folate-supplemented, PS and maternal-folate-supplemented, MS) for four weeks. They were mated and grouped accordingly: $PS{\times}MS$, $PS{\times}MD$, $PD{\times}MS$, and $PD{\times}MD$. Pups were killed on day 21 of lactation. The hepatic folate content was markedly reduced in the $PD{\times}MD$ and $PS{\times}MD$ and $PD{\times}MS$ as compared with the $PS{\times}MS$ group. The hepatic global DNA methylation was decreased in the $PD{\times}MS$ and $PS{\times}MD$ groups as much as in the $PD{\times}MD$ group, and all the three groups were significantly lower as compared to the $PS{\times}MS$ group. There were no significant differences in the hepatic FR${\alpha}$, IGF-2 and IGF-1R expressions among the groups. Positive correlations were found between the hepatic folate content and global DNA methylation and protein expressions of FR${\alpha}$, IGF-2 and IGF-1R, whereas an inverse correlation was found between hepatic folate content and plasma homocysteine level in the 3-week-old rat pup. The results of this study show that both paternal and maternal folate deficiency at mating can influence the folate content and global DNA methylation in the postnatal rat liver.

• 한국양식학회지
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• 제17권1호
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• pp.62-68
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• 2004

A cDNA encoding the masu salmon, Oncorhynchus masou, estrogen receptor $\alpha$ (msER$\alpha$) was cloned from the pituitary gland by polymerase chain reaction (PCR). This cDNA contains an open reading frame encoding 513 amino acid residues, and the calculated molecular weight of this protein is about 56,430 Dalton. The amino acid sequences of the DNA binding and ligand binding domains of msER$\alpha$ showed high homology to those of other fish species (84-100%). Reverse transcription PCR analysis showed that the mRNA level of msER$\alpha$ in the pituitary was slightly higher in estradiol-17$\beta$(E2) injected masu salmon than that of control fish. To test the biological activity of msER$\alpha$, the cDNA was ligated to a mammalian expression vector and transfected into a gonadotrope-derived cell line, L$\beta$T2, with a reporter plasmid including estrogen responsive element. Expression of the reporter protein, luciferase, was E2 and msER$\alpha$-dependent. The masu salmon ER$\alpha$ is structurally conserved among teleost species and functions as a transcriptional activator in the pituitary cells.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.1
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• pp.290.1-290.1
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• 2003

Oxidative DNA damage has been associated with many disease. Quantation of DNA adducts is considered to be a useful biomarker of oxidative DNA damage because its formation can also be induced by oxidative stress. Extensive efforts have been taken to identify the analytical methods for minimizing the artifactual formation of oxidative DNA damage. We have done direct analysis of DNA adducts using LC/ESI-MS without urine sample extraction. (omitted)

• Journal of Microbiology and Biotechnology
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• 제14권6호
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• pp.1280-1285
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• 2004

Retron is a prokaryotic genetic element, producing a short single-stranded DNA covalently linked to RNA (msDNA-RNA) by a reverse transcriptase (RT). In retron EC83, msDNA is further processed at between the 4th and the $5^{th}$ nucleotides, leaving a 79 nucleotide-long single-stranded DNA as a final product. To investigate this site-specific cleavage in msDNA synthesis, we purified the RT protein of retron EC83. Initially, RT ORF was cloned under the tac promoter, but the expression was very poor largely because of poor translation. In order to facilitate translation, the nucleotide sequence for the first nine amino acids was randomized with synonymous codons. This change of downstream sequence of translational initiation codon greatly affected the efficiency of translation. We could isolate clones which greatly increased RT production, and their sequences were compared to those of the low producers. The overproduced protein was purified and was shown to have RT activity.

• 한국환경보건학회:학술대회논문집
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• 한국환경보건학회 2002년도 춘계 국제 학술대회
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• pp.49-51
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• 2002

To identify and evaluate the dichlorobenzidine(DCB)-DNA adducts in liver cell and bladder epithelial cells by $^{32}$ P-postlabeling and GC/MS-SIM, we orally exposed the dichlorobenzidine (20mg/kh body wt.,/day)to male sprague-dawley rats for 14 days. Two kinds of DCB-DNA adduct were found at the same site of thin layer chromatogram of $^{32}$ P-postlabeling method in liver cells and bladder epithelial cells. In liver cells, relative adduct labeling(RAL) $\times$ 10$^{12}$ of DCB-DNA adduct A1 were 34.1$\pm$3.71 and 69.9$\pm$5.02, that of adduct A2 were 74.1$\pm$10.1 and 105.1$\pm$10.1 on 10 and 14 days after treatment, respectively. And in bladder epithelia cells, RAL $\times$ 10$^{12}$ of DCB-DNA adduct A1 were 5.92$\pm$1.60 and 15.9$\pm$1.31, that of adduct A2 were 9,81$\pm$2.81 and 22.8$\pm$1.79 on 10 and 14 days after treatment, respectively. DCB metabolites formed DNA adducts were monoacetyl-dichlorobenzidine(acDCB) and diacety1-dichlorobenzidine(di-acDCB), which was identify by gas chromatography/mass spectrometry-scan ionization mode(GC/MS-SIM), along with hydrolysis, extraction and TFA(trifluoroacetyl anhyride) derivatization with DCB-DNA adducts isolated from live cells and bladder epithelial cells. The base peak of acDCB were 252 and 294 m/z, and that of di-acDCB were 252, 294 and 336 m/z. In conclusion, the exposed DCB formed two kinds of DCB-DNA adduct, the proximate materials of that were acDCB and di-acDCB in liver and bladder epithlial cells. And the above GC/MS-SIM method was found the DCB-DNA adducts could be monitoring by gas chromatography.

• 한국환경보건학회지
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• 제28권1호
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• pp.21-29
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• 2002

To identify and evaluate the dichlorobenzidine(DCB)-DNA adducts in liver cell and bladder epithelial cells by $^{32}$ P-postlabeling and GC/MS-SIM, we orally exposed the dichlorobenzidine(20mg/kh body wt./day) to male Sprague-Dawley rats(l85$\pm$10g) for 14 days. Two kinds of DCB-DNA adduct(A1 and A2) were found at the same site of thin layer chromatogram of $^{32}$ P-postlabeling method in liver cells and bladder epithelial cells. In liver cells, relative adduct labeling(RAL) $\times$ 10$^{12}$ of DCB-DNA adduct A1 were 34.1$\pm$3.71 and 69.9$\pm$5.02, that of adduct A2 were 74.1$\pm$10.1 and 105.1$\pm$10.1 on 10 and 14 days after treatment, respectively. And in bladder epithelia cells, RAL $\times$ 10$^{12}$ of DCB-DNA adduct A1 were 5.92$\pm$1.60 and 15.9$\pm$1.31, that of adduct A2 were 9.81$\pm$2.81 and 22.8$\pm$1.79 on 10 and 14 days after treatment, respectively. DCB metabolites formed DNA adducts were monoacetyl-dichlorobenzidine(acDCB) and diacetyl-dichlorobenzidine(di-acDCB), which was identify by gas chromatography/mass spectrometry-scan ionization mode(GC/MS-SIM), after hydrolysis of DCB-DNA adducts isolated from live cells and bladder epithelial cells. The base peak of acDCB were 252 and 294 m/z, and that of di-acDCB were 252, 294 and 336 m/z. In conclusion, the exposed DCB formed two kinds of DCB-DNA adduct, the proximate materials of that were acDCB and di-acDCB in liver and bladder epithelial cells. And the above GC/MS-SIM method was found the DCB-DNA adducts could be monitoring by gas chromatography.

• 생명과학회지
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• 제21권3호
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• pp.385-392
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• 2011

국내에 서식하는 수달의 경우 멸종 위기 I 급 종으로 지정되어 국가적인 차원에서 관리하고 있는 보호종이다. 수달의 유전자원 보호 및 체계적인 관리를 위한 기초자료로 활용하기 위해 경남지역에 서식하는 수달의 계통유전학적 유연관계를 mtDNA D-loop 지역의 염기서열분석과 MS marker 분석을 통하여 실시하였다. 그 결과 mtDNA D-loop 지역의 676 bp 부분만 보았을 때 5개의 SNP가 확인되었으며, 6개의 haplotype이 추정되었다. 진주 인근 지역과 거제도 인근 지역에서 수집한 시료는 지역 내 유전적 거리가 지역 간의 유전적 거리보다는 가까운 것을 확인 할 수 있었고, 진주와 거제도 지역 간의 유전적 거리는 확연히 구분이 되었다. MrBays의 Bayesian Markov chain Monte Carlo 분석법을 이용하여 추정한 phylogeny 분석결과 뚜렷한 2개 그룹(진주와 거제/창녕 그룹)으로 분류 되었다. Parsimonious median-joining network [5] 분석의 결과 또한 2개의 뚜렷한 그룹으로 분류되어 phylogeny 분석결과와 일치하는 결과를 보였다. MS marker를 이용하여 추정한 유전적 거리지수를 활용하여 추정한 consensus tree의 결과 또한 크게 2개의 그룹으로 분류 되며, 첫 번째 그룹에는 거제도지역 시료, 진주인근지역 시료 일부 그리고 창녕 우포늪에서 채취한 시료가 하나의 그룹으로 나뉘어 졌으며, 두 번째 그룹에는 진주인근 지역에서 채취한 시료만이 포함되어 하나의 그룹을 형성하여, mtDNA를 이용하여 분석한 것과 일부 다른 결과를 보였다. 이러한 결과의 차이는 모계를 추정하는 mtDNA와 상염색체 상의 MS marker의 특성에 기인한 것으로 보이나, 경상남도에 서식하는 수달을 크게 진주와 거제지역의 수달로 구분하는 것에는 유사한 결과를 보여 서식지 별 유전적 고정현상이 있음을 확인할 수 있었다. 하지만 좀 더 정확한 검증을 위해서는 수달의 full mtDNA 분석 및 국내에서 서식하는 수달에 적합한 MS marker발굴을 통한 대립유전자형을 분석하는 추가 연구가 필요하며, 전국 단위의 수달 시료를 확보하여 유전적 유연관계 분석을 실시한다면 한국 내 수달의 보전 및 보호에 도움이 될 것으로 사료되어 진다.

• Journal of Periodontal and Implant Science
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• 제38권sup2호
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• pp.299-308
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• 2008

Purpose: The aim of this study was to evaluate adhesion and gene expression of the MC3T3-E1 cells cultured on machined titanium surface (MS) and anodized titanium surface (AS) using MTT test, Scanning electron micrograph and cDNA microarray. Materials and Methods: The MTT test assay was used for examining the proliferation of MC3T3-E1 cells, osteoblast like cells from Rat calvaria, on MS and AS for 24 hours and 48 hours. Cell cultures were incubated for 24 hours to evaluate the influence of the substrate geometry on both surfaces using a Scanning Electron Micrograph (SEM). The cDNA microarray Agilent Rat 22K chip was used to monitor expressions of genes. Results: After 24 hours of adhesion, the cell density on AS was higher than MS (p < 0.05). After 48 hours the cell density on both titanium surfaces were similar (p > 0.05). AS had the irregular, rough and porous surface texture. After 48 hours incubation of the MC3T3-E1 cells, connective tissue growth factor (CTGF) was up-regulated on AS than MS (more than 2 fold) and the insulin-like growth factor 1 receptor was down-regulated (more than 2 fold) on AS than MS. Conclusion: Microarray assay at 48 hours after culturing the cells on both surfaces revealed that osteoinductive molecules appeared more prominent on AS, whereas the adhesion molecules on the biomaterial were higher on MS than AS, which will affect the phenotype of the plated cells depending on the surface morphology.