• Molecules and Cells
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• v.19 no.2
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• pp.279-282
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• 2005

In mammals, 7-dehydrocholesterol reductase (Dhcr7) is the terminal enzyme in cholesterol biosynthesis. We previously reported that the Dhcr7 proximal promoter (-179 to +1), which contains CpG islands, is responsible for sterol-mediated expression of the rat gene. In the present study, we examined whether methylation of this region affects the transcriptional activity of the Dhcr7 gene. In vitro DNA methylation of the Dhcr7 promoter and luciferase-reporter assays showed that DNA methylation of the CpG islands suppressed transcription. Furthermore, treatment of the methylated Dhcr7 promoter with the demethylating agent, 5-aza-2'-deoxycytidine (5-Aza-CdR), reversed the suppression of promoter activity. These results indicate that methylation of the CpG islands is an important transcriptional regulatory mechanism in the Dhcr7 promoter.

• Korean Journal of Plant Taxonomy
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• v.41 no.3
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• pp.194-201
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• 2011

In order to acquire information on chloroplast DNA markers to evaluate the genetic diversity of evergreen broad leaved plants, we investigated the intraspecific variation of cpDNA in eight non-coding regions of nine species commonly distributed in East Asia. Although no variations were detected in psbA-trnH, rpoB-trnC, rpl16 and atpB-rbcL regions, a relatively large amount of intraspecific variations was detected in the psbC-trnS, rps16 and trnL-F regions. These results suggested that these three cpDNA markers are suitable to assess genetic diversity of the species investigated in this study. In contrast, intraspecific variations were detected in seven taxa except Hedera rhombea and Neolitsea aciculata. Neolitsea sericea and the taxa of Quercus had many polymorphic sites.

• Journal of Korean Society of Forest Science
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• v.99 no.3
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• pp.344-352
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• 2010

To investigate the mating system of clones in the seed orchard of Japanese red pine, parameters of mating system, such as outcrossing rates, number of potential pollen contributors, and degree of pollen contamination, were estimated in the seed orchard of Japanese red pines on the basis of DNA data including 4 nSSR and 6 cpSSR markers. Estimates of outcrossing rates were ranged from 94.9 to 100% with an average of 98.9% on the basis of the analysis of cpSSR haplotypes. They were ranged from 90.3% to 100% with an average of 95.9% on the basis of the analysis of nSSR genotypes. However, cross checking of both DNA markers revealed that the seeds presumed to be products of self pollination were turned out to be generated by pollination between mother tree and other tree (i.e., 100% of cumulative outcrossing rate). Estimates of pollen contamination ranged from 43.6% (Gangwon-10) to 56.4% (Gangwon-12) with the average of 48.9%. On the basis of pooled cpSSR haplotype of each seed, maximum number of 21 pollen contributors were verified from the seeds reproduced by Kyungbuk-38. Minimum number of 13 pollen contributors were verified in Gangwon-10. Mean of 16.2 pollen contributors were verified from a total of 5 mother trees. In conclusion, considering pretty high outcrossing rates between clones within a seed orchard, it may be expected that a fairly good genetic potential of the seeds, produced in '77 plot of the seed orchard of Japanese red pines at Anmyeon island, may be guaranteed. Observed results from the analysis of mating system of Japanese red pines in a '77 plot of the seed orchard may also provide useful information for the establishment and management of the seed orchard of the progressive generation.

• Journal of Plant Biotechnology
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• v.47 no.2
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• pp.141-149
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• 2020

Solanum hougasii, one of the wild Solanum species, has been widely used in potato breeding since it exhibits excellent resistance to diverse important pathogens. S. hougasii can be directly crossed with the cultivated tetraploid potato (S. tuberosum) owing to its EBN (Endosperm Balanced Number) value of 4, which is same as that of S. tuberosum although it is an allohexaploid. In this study, the complete chloroplast genome sequence of S. hougasii was obtained by next-generation sequencing technology, and compared with that of the chloroplast genome of seven other Solanum species to identify S. hougasii-specific PCR markers. The length of the complete chloroplast genome of S. hougasii was 155,549 bp. The structural organization of the chloroplast genome in S. hougasii was found to be similar to that of seven other Solanum species studied. Phylogenetic analysis of S. hougasii with ten other Solanaceae family members revealed that S. hougasii was most closely related to S. stoloniferum, followed by S. berthaultii, and S. tuberosum. Additional comparison of the chloroplast genome sequence with that of five other Solanum species revealed five InDels and 43 SNPs specific to S. hougasii. Based on these SNPs, four PCR-based markers were developed for the differentiation of S. hougasii from other Solanum species. The results obtained in this study will aid in exploring the evolutionary and breeding aspects of Solanum species.

• Journal of Plant Biotechnology
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• v.48 no.1
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• pp.18-25
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• 2021

Solanum demissum is one of the wild Solanum species originating from Mexico. It has wildly been used for potato breeding due to its resistance to Phytophthora infestans. S. demissum has an EBN value of four, which is same as that of S. tuberosum, so that it is directly crossable for breeding purposes with the cultivated tetraploid potato (S. tuberosum). In this study, the chloroplast genome sequence of S. demissum obtained by next-generation sequencing technology was described and compared with those of seven other Solanum species to develop S. demissum-specific markers. Thetotal sequence length of the chloroplast genome is 155,558 bp, and its structural organization is similar to those of other Solanum species. Phylogenetic analysis with ten other Solanaceae species revealed that S. demissum is most closely grouped with S. hougasii and S. stoloniferum followed by S. berthaultii and S. tuberosum. Additional comparison of the chloroplast genome sequence with those of seven other Solanum species revealed two InDels specific to S. demissum. Based on these InDels, two PCR-based markers for discriminating S. demissum from other Solanum species were developed. The results obtained in this study will provide an opportunity to investigate more detailed evolutionary and breeding aspects in Solanum species.

• Environmental Engineering Research
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• v.11 no.5
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• pp.277-284
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• 2006

The genetic toxicity of environmental pollutants, namely, nonylphenol (NP), bisphenol A (BPA) and chloropyriphos (CP) was investigated in aquatic sentinel species, freshwater crustacean, Daphnia magna, and larva of aquatic midge, Chironomus tentans, using Comet assay. Physiological effect of such pollutants was also investigated by studying the specimens' rates of reproduction, growth and survival. Acute toxicity results showed that, as expected, Daphnia was more sensitive than Chironomus to chemical exposure. The order of acute toxicity was CP > NP > BPA in D. magna and NP > CP > BPA in C. tentans. BPA may exert a genotoxic effect on D. magna and C. tentans, given that DNA strand breaks increased in both species exposed to this compound, whereas NP- and CP-induced DNA damage occurred only in C. tentans. In vivo genotoxic data obtained in aquatic sentinel species could provide valuable information for freshwater quality monitoring. The experiments with NP-exposed D. magna showed that the pollutant has long-term effects on reproduction, whereas no short-term effect on DNA integrity was found, being an example of a false-negative result from the biomarkers perspective. This result could be interpreted that other mechanism than genetic alteration might be involved in NP-induced reproduction failure in D. magna. False-positive results from the genotoxic biomarker obtained in BPA-exposed D. magna and in NP-exposed C. tentans make it difficult to use DNA integrity as an early warning biomarker. However, as the mere presence of genotoxic compounds, which are potentially carcinogenic, is of high concern to human and ecosystem health, it could also be important to rapidly and effectively detect genotoxic compounds in the aquatic system in ways that do not necessarily accompany a higher level of alteration. Considering the potential of D. magna and C. tentans as bioindicator species, and the importance of genotoxic biomarkers in ecotoxicity monitoring, DNA damage in these species could provide useful information for environmental risk assessment.

• Korean Journal of Plant Tissue Culture
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• v.22 no.3
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• pp.149-155
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• 1995

The coat protein (CP) gene was cloned from RNA genome of the Cucumber Mosaic Virus strain ABI (CMV-ABI) isolated in Korea. The comparisons of the nucleotide sequence of the cloned CP gene and its deduced amino acid sequences with other CP genes revealed that the CMV-ABI belongs to subgroup I (type I), CMV-ABI developed the typical mosaic symptom in infected plants. Tobacco plants (Samsun and NC82) were transformed by leaf-disc transformation via Agrobacterium, temefaciens LB4404 harboring pVCP, witch CMV-ABI CP gene was inserted into the pBI121, and a number of mature transgenic tobacco plants were developed. Southern and PCR analysis of genomic DNA from the transgenic plants showed that the CP gene was integrated into the genomes of the most of the transgenic plant. Result of the segregation patterns of resistance in T1 seedlings of the plants to kanamycin showed that the transgenic plants containing l,2 and 3 copies of CP gene were50%, 39% and 11% of the total transgenic plants, respectively.

• Molecules and Cells
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• v.27 no.3
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• pp.365-381
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• 2009

The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast MatK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi's original treatment of Megaleranthis saniculifolia to Trollius chosenensis Ohwi.

• Journal of Dairy Science and Biotechnology
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• v.30 no.1
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• pp.31-36
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• 2012

Lactobacillus rhamnosus GG(ATCC 53103) is one of the best researched probiotic strains in the world. Studies in children have shown that Lactobacillus rhamnosus GG effectively prevents early atopic disease in patients with high risk. The active molecules associated with the immunostimulatory sequence and anti-allergy effects of L. rhamnosus GG have not yet been identified. Unmethylated CpG motifs in bacterial DNA have a mitogenic effect in mouse immune cells, CpG-containing ISS oligodeoxynucleotides are potent Th1 adjuvants, effective in both preventing and reversing Th2-biased immune deviation in allergy models. The genomic DNA of L. rhamnosus GG is a potent inducer of murine B cell and dendritic cell immunoactivation. In L. rhamnosus GG genomic DNA, ID35 shows high activity in ISS assays in both mice and humans. The effects of ID35 result from a unique TTTCGTT motif located at its 5'-end, and its effects are comparable with murine prototype CpG 1826. L. rhamnosus GG is known to secrete proteinaceous pili encoded by the spaCBA gene cluster. The presence of pili structures may be essential for its adhesion to human intestinal mucus, explaining the prolonged duration of intestinal residence of this bacterium, compared to that of non-piliated lactobacilli.

• Clinical and Experimental Reproductive Medicine
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• v.37 no.1
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• pp.25-31
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• 2010

Objective: X inactivation is the silencing one of the two X chromosomes in female mammals for gene dosage on the X-chromosome between female and male. X inactivation is controlled by X inactive-specific transcript (XIST) gene, untranslated RNA. XIST is expressed only from the inactive X (Xi), not expressed from the active X (Xa). The Xist promoter is methylated on the silent Xist allele on the Xa in somatic cells, and less methylated on the Xist-expressing Xi. We investigated the difference of XIST methylation pattern of the promoter and 5'-region of XIST from male (XY) and female (XX) subjects. Methods: The direct quantification of XIST methylation is required for clinical application of normal XX and XY blood. Methylation percentage of eight CpG sites (-1696, -1679, -1475, -1473, -1469, +947, +956, +971) of XIST gene were diagnosed by pyrosequencing. Results: We directly quantitated the methylation percentage of the promoter and 5'-end of XIST by pyrosequencing. The average methylation percentages at CpG6-8 sites (+947, +956, +971) were 45.2% at CpG6, 49.9% at CpG7, and 44.2% at CpG8 from normal female and normal male were 90.6%, 96.7%, 87.8%, respectively. Nether CpG 1-5sites (-1696, -1679, -1475, -1473, -1469) had any effect on XX and XY. Conclusion: This method is sensitive for quantifying the small percentage change in the methylation status of XIST, and may be used for diagnosis.