• Genomics & Informatics
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• v.9 no.3
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• pp.136-137
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• 2011

Methylation of cytosine is a post-synthesis modification that does not affect the primary DNA sequence but greatly influences gene expression level and phenotypes of an organism. As high-throughput sequencing of bisulfite-treated DNA is the most efficient method to identify methylated sites, several tools to map sequencing reads on a reference are available. But tools to visualize and to interpret the methylation level of methylation sites are currently insufficient. Herein, we present a novel tool to visualize the methylation level of CpG sites.

• Korean Journal of Plant Taxonomy
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• v.43 no.1
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• pp.12-21
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• 2013

To clarify the taxonomic position for Astragalus nakaianus and provide correct scientific name for A. mongholicus cultivar in South Korea, we examined external morphological characters and sequence variations from ITS and five cp non-coding DNA regions. Genetic structure was also analyzed for 61 individuals from three populations using nine microsatellite loci. We found no significant difference between the South Korean cultivar and A. mongholicus var. dahuricus when morphology and ITS sequences were considered. Morphologically, A. nakaianus specimens varied somewhat from A. mongholicus var. mongholicus and var. dahuricus in habit, plant height, and lengths of leaf axis and leaflet. Although sequence data from ITS and cp noncoding DNA regions could not distinguished A. nakaianus from A. mongholicus, microsatellite analysis revealed strong structuring between the cultivar and A. nakaianus. Therefore, we conclude that the South Korean A. mongholicus cultivar should be treated as A. mongholicus var. dahuricus and that A. nakaianus should be merged into A. mongholicus as a variety, i.e., A. mongholicus var. nakaianus.

• Korean Journal of Plant Resources
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• v.25 no.1
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• pp.63-71
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• 2012

To assess parameters of mating system in seed orchard, such as outcrossing rates, number of potential pollen contributors, and degree of pollen contamination, seeds, produced in '77 plot of the Japanese red pine (Pinus densiflora S et Z) seed orchard at Anmyeon island, were collected in 2007 and analysed by nSSR and cpSSR markers. Estimates of outcrossing rates ranged from 91.2 to 100% (mean 97.7%) on the basis of the analysis of cpSSR haplotypes and from 81.6 to 100% (mean 95.3%) on the basis of the analysis of nSSR genotypes. By cross checking of both DNA markers, seeds, presumed to be products of self pollination on the basis of single marker, were confirmed as outcrossed seeds, which resulted in cumulative outcrossing rates of 98.9%. On the basis of pooled cpSSR haplotype of each seed, the number of pollen contributors and paternal contribution rates were estimated as 14.8 and 0.512, respectively. In conclusion, considering pretty high level of outcrossing rates observed in a seed orchard, good genetic potential of the seeds, produced in '77 plot of the seed orchard of Japanese red pines at Anmyeon island, may be guaranteed. Investigated results from the analysis of mating system of Japanese red pines in a '77 plot of the seed orchard may also be expected to provide useful information for the management and establishment of the seed orchard of the progressive generation.

• Proceedings of the Korean Society of Crop Science Conference
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• 2000.11a
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• pp.93-94
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• 2000

• 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.

• Proceedings of the Zoological Society Korea Conference
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• 2001.10a
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• pp.155.3-156
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• 2001

• Bioindustry News
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• v.14 no.4
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• pp.16-20
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• 2001

• Korean Journal of Plant Resources
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• v.25 no.4
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• pp.490-497
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• 2012

Phylogenetic analyses were conducted to evaluate relationships of 5 taxa of Korean Hydrocotyle, H. spp. found in the Ulleung island including one outgroup (Centella asiatica). The molecular phylogenetic methods based on nuclear ribosomal DNA ITS region and cpDNA trnH-psbA region. Centella asiatica was used outgroup for analysis. As the result, genus Korean Hydrocotyle were grouped by 94% bootstrap value. Korean Hydrocotyle was grouped by four clades; Clade I-H. maritima, H. sibthorpides and H. yabei clade Clade II-H. nepalensis clade clade III-H. ramiflora clade clade IV-H. spp. clade. H. maritima, H. sibthorpides and H. yabei was not distinguished, seperately. H. spp. was distinctly distinguished other Korean Hydrocotyle.

• Journal of the Korean Society of Tobacco Science
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• v.20 no.1
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• pp.66-70
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• 1998

TMV resistant lines (TRLs) originated from the Blo plant of Nicotiana tabacum cv. NC82 transformed with TMV coat protein cDNA which initially showed delayed disease symptom were selected for increased resistance in each subsequent generation. The result of field experiment of the transgenic tobacco lines in the fifth generation for TMV resistance and their response to other tobacco diseases (black shank, bacterial wilt, and powdery mildew) is described in this report. When fifteen TRLs of the fifth generation were tested for TMV resistance by mechanically inoculating the individual plants, over 95 percent of the plants of 6 lines showed complete resistance even 8 weeks after the inoculation. Average frequency of the resistant plants in TRLs of the fifth generation 8 weeks after the inoculation was 87%. Stable insertion and expression of TMV coat protein cDNA in the fifth generation of the transgenic tobacco plant were confirmed by PCR and immunoblot hybridization, respectively. All TRLs were resistant to the black shank but were susceptible to the bacterial wilt disease and the powdery mildew to the same degree as non-transgenic NC82 was. Therefore, it was indicated that the phenotypes related at least to disease resistance were not changed in the transgenic tobacco. Key words : TMV CP cDNA, TMV resistant tobacco plant, transformation.

• Reproductive and Developmental Biology
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• v.34 no.3
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• pp.181-184
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• 2010

Osmolarity of culture media is one of the most important factors affecting in vitro development. This study was conducted to investigate the DNA methylation status of Pre-1 and satellite sequence in pig nuclear transfer (pNT) embryos produced under different osmolarity culture conditions. Control group of pNT embryos was cultured in PZM-3 for six days. Other two treatment groups of pNT embryos were cultured in modified PZM-3 with 138 mM NaG or 0.05M sucrose (mPZM-3, 320 mOsmol) for two days, and then cultured in PZM-3 (270 mOsmol) for four days. Previous our studies have reported that pNT embryos cultured in both hypertonic media showed significantly higher blastocyst formation rate than that of control. The DNA methylation status of the satellite sequences in blastocyst was characterized using bisulfite-sequencing technology. The satellite region had a similar methylation pattern of in vivo blastocyst among two culture groups excepting the control group. Each level of methylation is that the satellite DNA moderately methylated (43.10% of PZM-3; 56.12% of NaCl; 55.06% of sucrose; 60.00% of in vivo embryos). As a result of the sequence of PRE-1, CpG methylation pattern was similar to three groups, including in vivo group. In case of the satellite DNA region, the osmolarity conditions were affected CpG DNA methylation status while PRE-1 sequence was not affected CpG DNA methylation in pNT blastocyst stage. These results indicate that the modification of osmolarity in a culture media may influence to spatially change of DNA methylation of repetitive sequence for pNT embryo development.