• Genomics & Informatics
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• v.8 no.1
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• pp.58-61
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• 2010

CpG is the pair of nucleotides C and G, appearing successively, in this order, along one DNA strand. It is known that due to biochemical considerations CpG is relatively rare in most DNA sequences. However, in particular subsequences, which are a few hundred to a few thousand nucleotides long, the couple CpG is more frequent. These subsequences, called CpG islands, are known to appear in biologically more significant parts of the genome. The ability to identify CpG islands along a chromosome will therefore help us spot its more significant regions of interest, such as the promoters or 'start' regions of many genes. In this respect, I developed the CpG islands search tool, CpG Islands Detector, which was implemented in JAVA to be run on any platform. The window-based graphical user interface of CpG Islands Detector may facilitate the end user to employ this tool to pinpoint CpG islands in a genomic DNA sequence. In addition, this tool can be used to highlight potential genes in genomic sequences since CpG islands are very often found in the 5' regions of vertebrate genes.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1232-1236
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• 2013

The Cu cation binding sites of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex have been investigated to explain the $[Cu{\cdot}DNA]$ biological activity caused by the Cu association to DNA. The structure of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex was investigated by electrospray ionization mass spectrometry (ESI-MS). The fragmentation patterns of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex were analyzed by MS/MS spectra. In the MS/MS spectra of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex, three fragment ions were observed with the loss of d(CpG), {d(CpG) + Cyt}, and {d(CpG) + Cyt + dR}. The Cu cation binds to d(CpG) mainly by substituting the $H^+$ of phosphate group. Simultaneously, the Cu cation prefers to bind to a guanine base rather than a cytosine base. Five possible geometries were considered in the attempt to optimize the $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex structure. The ab initio calculations were performed at B3LYP/6-31G(d) level.

• Journal of Life Science
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• v.18 no.8
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• pp.1132-1139
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• 2008

A CpG island is a short stretch of DNA in which the frequency of the CG dinucleotide is higher than other regions. CpG islands are present in the promoters and exonic regions of approximately $30{\sim}60$% of mammalian genes so they are useful markers for genes in organisms containing 5-methylcytosine in their genomes. Recent evidence supports the notion that the hypermethylation of CpG island, by silencing tumor suppressor genes, plays a major causal role in cancer, which has been described in almost every tumor types. In this respect, CpG island search by computational methods is very helpful for cancer research and computational promoter and gene predictions. I therefore developed a window program (called CpGi) on the basis of CpG island criteria defined by D. Takai and P. A. Jones. The program 'CpGi' was implemented in Visual C++ 6.0 and can determine the locations of CpG islands using diverse parameters (%GC, Obs (CpG)/Exp (CpG), window size, step size, gap value, # of CpG, length) specified by user. The analysis result of CpGi provides a graphical map of CpG islands and G+C% plot, where more detailed information on CpG island can be obtained through pop-up window. Two human contigs, i.e. AP00524 (from chromosome 22) and NT_029490.3 (from chromosome 21), were used to compare the performance of CpGi and two other public programs for the accuracy of search results. The two other programs used in the performance comparison are Emboss-CpGPlot and CpG Island Searcher that are web-based public CpG island search programs. The comparison result showed that CpGi is on a level with or outperforms Emboss-CpGPlot and CpG Island Searcher. Having a simple and easy-to-use user interface, CpGi would be a very useful tool for genome analysis and CpG island research. To obtain a copy of CpGi for academic use only, contact corresponding author.

• IMMUNE NETWORK
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• v.12 no.3
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• pp.89-95
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• 2012

Immune cells express toll-like receptors (TLRs) and respond to molecular patterns of various pathogens. CpG motif in bacterial DNA activates innate and acquired immune systems through binding to TLR9 of immune cells. Several studies reported that CpG can directly regulate B cell activation, differentiation, and Ig production. However, the role of CpG in B cell growth and Ig production is not fully understood. In this study, we analyzed the effect of CpG on the kinetics of mouse B cell viability, proliferation, and Igs production. Overall, CpG enhanced mouse B cell growth and production of Igs in a dose-dependent manner. Unlike LPS, 100 nM CpG (high dose) did not support TGF-${\beta}1$-induced IgA and IgG2b production. Moreover, 100 nM CpG treatment abrogated either LPS-induced IgM or LPS/TGF-${\beta}1$-induced IgA and IgG2b production, although B cell growth was enhanced by CpG under the same culture conditions. We subsequently found that 10 nM CpG (low dose) is sufficient for B cell growth. Again, 10 nM CpG did not support TGF-${\beta}1$-induced IgA production but, interestingly enough, supported RA-induced IgA production. Further, 10 nM CpG, unlike 100 nM, neither abrogated the LPS/TGF-${\beta}1$- nor the LPS/RA-induced IgA production. Taken together, these results suggest that dose of CpG is critical in B cell growth and Igs production and the optimal dose of CpG cooperates with LPS in B cell activation and differentiation toward Igs production.

• Molecular & Cellular Toxicology
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• v.5 no.3
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• pp.207-215
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• 2009

Despite wide therapeutic use of CpG ODN against infection, allergy and cancer, the safety and toxicity of CpG ODNs were poorly delineated. Thus, we investigated whether optimal dosing of CpG ODN would affect immunotoxicological parameters in NZB/NZW F1 mice. Comparisons were made among control, non-CpG ODN and mouse CpG ODN ($10{\mu}g$)-treated groups for 4 weeks. To gauge the immunotoxicity of CpG ODNs, we measured nonspecific parameters, degree of lupus nephritis, proteinuria, or autoantibody, and cytokine expression in mRNA level of lymphocytes. We found that there were no significant differences among groups in nonspecific immunotoxicological profiles and in evaluation profiles of glomerulonephritis. However, titer of anti-dsDNA and anti-cardiolipin antibodies in mouse CpG ODN group rose three or eight-fold higher than in control group. Collectively, CpG ODN might be clinically less immunotoxic in terms of clinical profiles in lupus-prone NZB/NZW F1 mice, in spite of high autoantibody titer in CpG ODN treated groups.

• Tuberculosis and Respiratory Diseases
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• v.50 no.1
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• pp.12-28
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• 2001

Background and Object : Immunostimulatory CpG-oligodeoxynucleotides (ISS CpG-ODN) up-regulate the $T_{H1}$-type immune response and down-regulate the $T_{H2}$-type response. This study was performed to investigate the immune response changes resulting from ISS CpG-ODN on bronchial hyperresponsiveness, eosinophilic inflammation and mucus hypersecretion in rat asthma. Materials and Methods : 10 normal controls(NC) and 26 asthmatic rats, which were generated by ovalbumin(OVA) sensitization and challenge, were studied. The asthmatic rats were randomized into 11 asthma controls(AC) and 15 in the asthma-CpG treatment group(CpG). The CpG group was administered ISS CpG-ODN intramuscularly and the AC group was administered a placebo(0.9% NaCl) on day 15 and 20. After CpG-ODN or placebo administration, we measured the IFN-${\gamma}$($T_{H1}$-type cytokine) and IL-4($T_{H2}$-type cytokine) levels in the bronchoalveolar lavage fluid(BALF), the specific airway resistance(sRaw), eosinophilic fraction in BALF, eosinophilic infiltration, goblet cell dysplasia and MUC5AC gene expression in the lung tissue. Results : In the BALF of the CpG group, the IFN-${\gamma}$ concentration was significantly high and the IL-4 concentration was significantly low when compared with the AC group. Both the sRaw and eosinophilic fraction, and infiltration into the BALF and lung tissue significantly lower in the CpG group when compared with the AC group. However, little difference in goblet cell dysplasia and MUC5AC gene expression was observed between the CpG group and the AC group. Conclusion : ISS CpG-ODN decreases bronchial hyperresponsiveness and eosinophilic inflammation in the rat asthma model through the up-regulation of the $T_{H1}$-type immune response with the down-regulation of the $T_{H2}$-type response. However, the effect of these immune response changes on mucus hypersecretion was is not remarkable in this study.

• Clinical and Experimental Pediatrics
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• v.48 no.3
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• pp.251-259
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• 2005

Atopy is a highly prevalent and serious health problem. The prevalence and severity of asthma and allergic diseases have increased over recent decades, particularly in industrialized nations. Early life infections may protect against the development of atopy and allergic diseases like asthma. The inverse relationship between the incidence of atopy and childhood infections has led to the 'hygiene hypothesis', which suggests that diminished exposure to childhood infections in modern society has led to decreased Th1-type responses. Th1 and Th2 responses are counter-regulatory. Reduced Th1 may lead to enhanced Th2-type inflammation, which is important in promoting asthma and allergic disease via up-regulation of IL-4, IL-5, and IL-13. It is now widely accepted that altered regulation of Th2 responses(and possibly the balance between Th1 and Th2 responses) is an important factor in the development of atopy. CpG DNA represent a novel class of drugs with substantial immunomodulatory properties. CpG DNA contain unmethylated motifs centered on the CpG dinucleotides, like bacterial DNA. These CpG DNA promote Th1 and regulatory type immune responses and suppress Th2 responses. In murine studies, CpG DNA are effective in prevention and treatment of asthma and allergic diseases. CpG DNA are just beginning to be tested in human asthma. While its precise mechanisms continue to be fully studied, CpG DNA offers considerable promise as a novel treatment for atopic inflammation. It may prove to be an important disease modifying therapy, or even curative therapeutic agent for asthma and allergic diseases.

• Molecular & Cellular Toxicology
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• v.3 no.1
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• pp.46-52
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• 2007

In the course of novel TLR (Toll like receptor) 9 ligand, we found novel CpG ODN (Oligodeoxynucleotide) was active in augmenting antibody in mice. However, immune mechanism of new CpG ODNs is unclear. To clarify this, we examined immunoadjuvanticity by employing in vitro and in vivo immune profiles. In brief, in vitro treatment of novel CpG ODN upregulated the expression of TNF-$\alpha$, IL-6, and IL-12 mRNA in macrophages as well as that of IFN-$gamma$ mPNA in mouse splenocytes. In parallel, in vivo injection of novel CpG ODN directly activates macrophages and splenocytess, consequently upregulating MHC class II and CD86. Finally, we demonstrated anti-HBs antibody augmentation of novel CpG ODN. Collectively, this data indicates that novel CpG ODN is immunoadjuvant armed with Th1 typed immune machinery.

• Fisheries and Aquatic Sciences
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• v.10 no.1
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• pp.1-7
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• 2007

The induction of cellular and humoral immunity and cytokine gene expression by synthetic CpG oligodexoynucleotides (CpG-ODNs) has not been investigated systematically in olive flounder Paralichthys olivaceus in vivo. We optimized the proper concentration of CpG-ODNs using an in vitro assay for the superoxide anion $(O_2^-)$. CpG-ODNs induced $O_2^-$ and nitric oxide (NO) production, lysozyme activity, and the proinflammatory cytokine gene expression of $IL-1{\beta}$ and $TNF-{\alpha}$ in olive flounder significantly in vivo, whereas non-CpG-ODNs did not produce these effects or produced them to a lesser extent. This implied that CpG-ODNs could stimulate cellular and humoral immunity and cytokine gene expression in olive flounder. This is the first evidence of NO production and the first study on the mRNA expression of the proinflammatory cytokine genes $IL-1{\beta}$ and $TNF-{\alpha}$ in olive flounder in response to CpG-ODNs. Comparison of the variation in NO production and lysozyme activity to that of other studies led us to postulate that a group-specific difference exists in the immune responses of olive flounder against CpG-ODNs. Furthermore, the detailed immunostimulatory spectrum of CpG-ODNs in olive flounder could be a useful index with which to analyze the effect of CpG-ODNs against the challenge test prior to field applications.

• Clinical and Experimental Pediatrics
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• v.45 no.7
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• pp.875-883
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• 2002

Purpose : Airways eosinophilia and increased IgE, characteristic features of asthma, result from a predominant Th2 response. In this study, we investigated the effect of CpG oligodeoxynucleotides (ODNs) on the inhibition of airways eosinophilia in mice with established airway inflammation. We also investigated the immunological mechanisms involved. Methods : Groups of BALB/c mice were sensitized intradermally with ovalbumin(OVA). At week 10, airway inflammation was induced by intranasal challenge of the mice with OVA. At week 14, the mice were challenged intranasally again with OVA in the presence and without the presence of CpG ODNs. Mice with saline administration served as negative controls. Bronchoalveolar lavage fluids(BALF) were obtained and eosinophils were counted. Th1 and Th2 cytokines in the spleen cell cultures were measured by ELISA. Serum OVA-specific IgE and IgG2a antibodies were also measured by ELISA. Results : BALF eosinophils were significantly inhibited in the CpG ODNs-treated mice(P<0.01). IgE and IgG2a levels increased significantly in both CpG ODNs-treated and untreated groups as compared to the negative control group; there was, however, no significant difference between the two groups four days after intranasal administration of CpG ODNs. Cytokine analysis revealed decreased production of IL-4, IL-5, and IL-13 and increased production of IL-12 in the CpG ODNs-treated group as compared to the untreated group. Interestingly, $IFN-{\gamma}$ levels were not upregulated in the CpG ODNs-treated group. Conclusion : CpG ODNs vaccination is a potentially useful approach for reversing airways eosinophilia in mice with established airways inflammation.