• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.3
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• pp.191-195
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• 2000

Quantitation of N7-methyldeoxyguanosine (N7-MedG) produced in the in vitro N-methly-N-nitrosuourea (NMU) action on thymus DNA has been achieved by enzymatic degradation, liquid chromatoraphic separaphic separation and desorption chemical ionization tandem mass spectrometry. In conjunction with the resolving power HPLC in the separation of isomers, desorprion chemical ionization tandem mass spectrometry has utilized in determining modified nucleosides at low levels using a stable-isotope labled compound as an internal reforence. The quantitative estimation of N7-methyldeoxyguanosine was previously established by an independent HPLC analysis of methylated calf thymus DNA. A sensitive and specific methodogy for the quantitation of N7-MedG at the picomole level using HPLC combined with tandem mass spectrometry without radioisotope labeling process is presented. The potential of the liquid chromatoraphic tandem mass exposure to methlation agents in vitro.

• Korean Journal of Clinical Laboratory Science
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• v.44 no.4
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• pp.167-177
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• 2012

Next-Generation Sequencing (NGS) is a term that means post-Sanger sequencing methods with high-throughput sequencing technologies. NGS parallelizes the sequencing process, producing thousands or millions of sequences at once. The latest NGS technologies use even single DNA molecule as a template and measures the DNA sequence directly via measuring electronic signals from the extension or degradation of DNA. NGS is making big impacts on biomedical research, molecular diagnosis and personalized medicine. The hospitals are rapidly adopting the use of NGS to help to patients understand treatment with sequencing data. As NGS equipments are getting smaller and affordable, many hospitals are in the process of setting up NGS platforms. In this review, the progress of NGS technology development and action mechanisms of representative NGS equipments of each generation were discussed. The key technological advances in the commercialized platforms were presented. As NGS platforms are a great concern in the healthcare area, the latest trend in the use of NGS and the prospect of NGS in the future in diagnosis and personalized medicine were also discussed.

• Journal of Microbiology
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• v.37 no.4
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• pp.224-228
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• 1999

Benzaldehyde dehydrogenase (BZDH), an enzyme involved in the degradation of toluene and xylenes, is encoded by the phnN gene of Pseudomonas sp. strain DJ77. We determined the nucleotide sequence of a DNA fragment of 1,803 base pairs which included the phnN gene. The fragment contained an open reading frame of 1,506 base pairs to accommodate th 55 kDa sized enzyme encoding BZDH. The enzyme efficiently oxidized benzaldehyde, salicylaldehyde, m-tolualdehyde and ps-tolualdehyde.

• Journal of Microbiology and Biotechnology
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• v.16 no.3
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• pp.391-398
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• 2006

$NF-{\kappa}B$ is a transcription factor involved in the innate immunity against bacterial infection and inflammation. It is also known to render cells resistant to the apoptosis caused by some anticancer drugs. Such a chemoresistance of cancer cells may be related to the activation of $NF-{\kappa}B$ transcription factor; however, the mechanism of activation is not well understood. Here, we demonstrate that a chemotherapeutic agent, etoposide, independently stimulates the $I{\kappa}B{\alpha}$ degradation pathway and PI3-kinase/Akt signaling pathway: The classical $I{\kappa}B{\alpha}$ degradation pathway leads to the nuclear translocation and DNA binding of p65 subunit through $IKK{\beta}$ kinase, whereas the PI3-kinase/Akt pathway plays a distinct role in activating this transcription factor. The PI3-kinase/Akt pathway acts on the p50 subunit of the $NF-{\kappa}B$ transcription factor and enhances the DNA binding affinity of the p50 protein. It may also explain the role of the PI3-kinase/Akt pathway in the anti-apoptotic function of $NF-{\kappa}B$ during chemoresistance of cancer cells.

• Interdisciplinary Bio Central
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• v.3 no.2
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• pp.8.1-8.6
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• 2011

Background: Thanks to the development of the mathematical/statistical reverse engineering and the high-throughput measuring biotechnology, lots of biologically meaningful genegene interaction networks have been revealed. Steady-state analysis of these systems provides an important clue to understand and to predict the systematic behaviours of the biological system. However, modeling such a complex and large-scale system is one of the challenging difficulties in systems biology. Results: We introduce a new stochastic modeling approach that can describe gene regulatory mechanisms by dividing two (DNA and protein) layers. Simple queuing system is employed to explain the DNA layer and the protein layer is modeled using G-networks which enable us to account for the post-translational protein interactions. Our method is applied to a transcription repression system and an active protein degradation system. The steady-state results suggest that the active protein degradation system is more sensitive but the transcription repression system might be more reliable than the transcription repression system. Conclusions: Our two layer stochastic model successfully describes the long-run behaviour of gene regulatory networks which consist of various mRNA/protein processes. The analytic solution of the G-networks enables us to extend our model to a large-scale system. A more reliable modeling approach could be achieved by cooperating with a real experimental study in synthetic biology.

• BMB Reports
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• v.48 no.7
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• pp.367-368
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• 2015

It has long been thought that glucocorticoid receptor (GR) functions as a DNA-binding transcription factor in response to its ligand (a glucocorticoid) and thus regulates various cellular and physiological processes. It is also known that GR can bind not only to DNA but also to mRNA; this observation points to the possible role of GR in mRNA metabolism. Recent data revealed a molecular mechanism by which binding of GR to target mRNA elicits rapid mRNA degradation. GR binds to specific RNA sequences regardless of the presence of a ligand. In the presence of a ligand, however, the mRNA-associated GR can recruit PNRC2 and UPF1, both of which are specific factors involved in nonsense-mediated mRNA decay (NMD). PNRC2 then recruits the decapping complex, consequently promoting mRNA degradation. This mode of mRNA decay is termed "GR-mediated mRNA decay" (GMD). Further research demonstrated that GMD plays a critical role in chemotaxis of immune cells by targeting CCL2 mRNA. All these observations provide molecular insights into a previously unappreciated function of GR in posttranscriptional regulation of gene expression. [BMB Reports 2015; 48(7): 367-368]

• Journal of Periodontal and Implant Science
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• v.41 no.3
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• pp.157-163
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• 2011

Purpose: Curcumin is known to exert numerous biological effects including anti-inflammatory activity. In this study, we investigated the effects of curcumin on the production of interleukin-6 (IL-6) by murine macrophage-like RAW 264.7 cells stimulated with lipopolysaccharide (LPS) from Prevotella intermedia, a major cause of inflammatory periodontal disease, and sought to determine the underlying mechanisms of action. Methods: LPS was prepared from lyophilized P. intermedia ATCC 25611 cells by the standard hot phenol-water method. Culture supernatants were collected and assayed for IL-6. We used real-time polymerase chain reaction to detect IL-6 mRNA expression. $I{\kappa}B-{\alpha}$ degradation, nuclear translocation of NF-${\kappa}B$ subunits, and STAT1 phosphorylation were characterized via immunoblotting. DNA-binding of NF-${\kappa}B$ was also analyzed. Results: Curcumin strongly suppressed the production of IL-6 at both gene transcription and translation levels in P. intermedia LPS-activated RAW 264.7 cells. Curcumin did not inhibit the degradation of $I{\kappa}B-{\alpha}$ induced by P. intermedia LPS. Curcumin blocked NF-${\kappa}B$ signaling through the inhibition of nuclear translocation of NF-${\kappa}B$ p50 subunit. Curcumin also attenuated DNA binding activity of p50 and p65 subunits and suppressed STAT1 phosphorylation. Conclusions: Although further study is required to explore the detailed mechanism of action, curcumin may contribute to blockade of the host-destructive processes mediated by IL-6 and appears to have potential therapeutic values in the treatment of inflammatory periodontal disease.

• The Korean Journal of Zoology
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• v.32 no.4
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• pp.305-313
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• 1989

The present investigation aims at inquiring into a possible target for the heat inactivation of SCK tumor cells by comparing the kinetics of cell survival, rate of protein synthesis, and DNA polymerase activity in the presence of heat protector or heat sensitirer. A possible conclusion to be drawn from the present experiment is that there is no direct correlation between cell death and decrease in the rate of protein synthesis, but that the loss of DNA polvmerase $\beta$ activity correlates quite well with cell inactivation. Thus, protein degrada-tion and/or abnormal protein synthesis causes cell inactivation innireuv, possibly by altering the cellular environment which in turn affects the DNA polymerase $\beta$ activity. Accordingly, further studies, dealing with the correlation between changes in the cellular environment and DNA polymerase $\beta$ activity, are needed to set insight into a possible target for the heat inactivation of cells. 본 연구는 열보호제 또는 열증감제의 존재하에서 세포 생존곡선, 단백질 합성률, DNA 중합효소 $\beta$의 활성변화를 비교 검토함으로써 SCK 종양세포가 열에 의해서 불활성화될 때의 표적이 무엇인지를 밝혀보기 위해서 수행되었다. 본 실험의 결과로 추정하건대 열에 의한 세포치사는 단백질 합성률의 변화와는 직접적인 연관성이 없으나, DNA 중합효소 $\beta$의 활성도와는 밀접한 연관성이 있음을 알 수 있다. 즉, 단백질의 분해 또는 비정상적인 단백질의 합성이 세포의 환경을 변화시키고 이것이 DNA 중합효소 $\beta$의 활성에 영향을 미침으로써 간접적으로 세포의 치사를 초래할 것으로 짐작할 수 있다. 따라서, 세포의 열불화성화의 표적을 좀더 분명히 밝히기 위해서는 세포의 환경변화와 DNA 중합효소 $\beta$의 활성과의 관계를 추구하는 연구가 수행되어야 할 것으로 사료된다.

• Microbiology and Biotechnology Letters
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• v.31 no.1
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• pp.25-31
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• 2003

Delftia acidovorans 51-A isolated from river water degrades aniline. In order to clone genes involved in aniline degradation, transposon Tn5-B20 was inserted into the strain 51-A to generate a mutant strain 10-4-2 that cannot utilize aniline as a carbon source. The mutant strain was not an auxotroph but could not degrade aniline. Southern hybridization analysis indicated that the transposon was inserted into the mutant bacterial DNA as a single copy. Flanking DNA fragment of Tn5-B2O insertion was cloned and sequenced. DNA sequence analysis revealed three ORFs encoding TdnQ, TdnT, and TdnA 1 that arc responsible for catechol formation from aniline through oxidative deamination. The analysis also confirmed that Tn5-B2O was inserted at the immediate downstream of tdnA1. The result suggests that the transposon insertion behind tdirA1 disrupted the pathway of the catechol formation from aniline, resulting in the mutant phenotype, which cannot degrade aniline. A large plasmid over 100-kb in size was detected from D. acidovorans 51-A and Southern hybridization analysis with Tn5-B2O probe showed that the transposon was inserted on the plasmid named pTDN51. Our results indicated that the tdn genes on pTDN51 of D. acidovorans 51-A are involved in aniline degradation.

• Korean Journal of Microbiology
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• v.37 no.3
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• pp.189-196
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• 2001

Eighty-seven microbial strains capable of growing on bisphenol A (BPA) as a sole carbon source were isolated from soils, waste waters and sludges. Among them, three bacterial strains were finally selected as potential decomposers through measuring BPA-degradation efficiency by HPLC analysis. Two of these bacterial strains were identified as Serratia marcescens 1901 and S. marcescens 1902, and another was Pseudomonas putida 1401 by 16S rDNA partial sequences and based on morphological and physiological properties. They showed higher cell growth and BPA degradation in PAV (PAS medium containing vitamin mixtures) than in PAS medium. The degradation efficiencies of these bacterial strains were within a range of 20-40% in the PAV containing 500 mg/1 or 100 mg/l of BPA fur 3 days. S. marcescens 1901 showed higher degradation efficiency at 100 mg/1 of BPA than those of other selected strains, while S. marcescens 1902 and P. putida 1401 degraded a high concentration of BPA (500 mg/l) with a degradation efficiency of 40% for 3 days. The BPA degradation using a mixed culture of three selected strains showed the similar level of dog-radation efficiency with that using a pure culture.