• Genomics & Informatics
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• v.5 no.4
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• pp.143-151
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• 2007

To understand the mechanism of transcriptional regulation, it is essential to detect promoters and regulatory elements. Various kinds of methods have been introduced to improve the prediction accuracy of regulatory elements. Since there are few experimentally validated regulatory elements, previous studies have used criteria based solely on the level of scores over background sequences. However, selecting the detection criteria for different prediction methods is not feasible. Here, we studied the calibration of thresholds to improve regulatory element prediction. We predicted a regulatory element using MATCH, which is a powerful tool for transcription factor binding site (TFBS) detection. To increase the prediction accuracy, we used a regulatory potential (RP) score measuring the similarity of patterns in alignments to those in known regulatory regions. Next, we calibrated the thresholds to find relevant scores, increasing the true positives while decreasing possible false positives. By applying various thresholds, we compared predicted regulatory elements with validated regulatory elements from the Open Regulatory Annotation (ORegAnno) database. The predicted regulators by the selected threshold were validated through enrichment analysis of muscle-specific gene sets from the Tissue-Specific Transcripts and Genes (T-STAG) database. We found 14 known muscle-specific regulators with a less than a 5% false discovery rate (FDR) in a single TFBS analysis, as well as known transcription factor combinations in our combinatorial TFBS analysis.

• Journal of Korean Library and Information Science Society
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• v.37 no.3
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• pp.173-191
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• 2006

Examinations and analysis were done to understand the digital reference services of the Teaching & Learning Aid Centers under 16 metropolitan city and provincial offices of education. The data used were collected from July 3. 2006 to July 15. 2006 by the direct contacts on their main homepages and recording the question and answer transcripts. It was proven that 13 of the 16 Teaching & Learning Aid Centers have done the reference services. In this study, several characteristics-whether the digital reference service was done or not, interface access level, its title, its communication tool, reference question number, reference question style, answer rate, etc-were analyzed. Tips for the future development were provided on the basis of the inadequacies and other findings revealed through this study.

• BMB Reports
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• v.39 no.1
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• pp.37-45
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• 2006

Bulked segregant analysis (BSA) and AFLP were used for isolation of genomic sex determination markers in Penaeus monodon. A total of 256 primer combinations were tested against 6-10 bulked genomic DNA of P. monodon. Five and one candidate female- and male-specific AFLP fragments were identified. Female-specific fragments were cloned and further characterized. SCAR markers derived from FE10M9520, FE10M10725.1, FE10M10725.2 and FE14M16340 provided the positive amplification product in both male and female P. monodon. Further analysis of these markers using SSCP and genome walk analysis indicated that they were not sex-linked. In addition, sex-specific (or differential) expression markers in ovaries and testes of P. monodon were analyzed by RAP-PCR (150 primer combinations). Twenty-one and fourteen RAP-PCR fragments specifically/differentially expressed in ovaries and testes of P. monodon were successfully cloned and sequenced. Expression patterns of 25 transcripts were tested against the first stranded cDNA of ovaries and testes of 3-month-old and broodstock-sized P. monodon (N = 5 and N = 7 - 10 for females and N = 4 and N = 5 - 7 for males, respectively). Five (FI-4, FI-44, FIII-4, FIII-39 and FIII-58) and two (M457-A01 and MII-51) derived RAP-PCR markers revealed female- and male-specific expression patterns in P. monodon. Surprisingly, MII-5 originally found in testes showed a higher expression level in ovaries than did testes of juvenile shrimps but a temporal female-specific pattern in P. monodon adults.

• BMB Reports
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• v.39 no.1
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• pp.26-36
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• 2006

Differential Display PCR technique (DD-PCR) was used for the analysis of altered gene expression in hemocytes of Vibrio harveyi-infected Penaeus monodon. Forty-four combinations of arbitrary and oligo(dT) primers were used to screen for differentially expressed genes. A total of 79 differentially expressed bands could be identified from 33 primer combinations. These included 48 bands (61%) whose expression level increased and 31 bands (39%) decreased after V. harveyi challenge. Subsequently, forty-eight differential display fragments were successfully reamplified and cloned. A total of 267 clones were randomly selected and sequenced. The sequence analysis showed that 85 (31%) out of 267 clones were matched with sequences in the GenBank database which represented 24 different genes with known functions. Among the known genes, glucose transporter 1, interferon-related developmental regulator 1, lysozyme, profilin, SERPINB3, were selected for further confirmation of their differentially expression patterns by real-time PCR. The results showed increasing in expression level of the selected genes in shrimp hemocytes after microbial challenge suggesting the involvement of such genes in bacterial response in shrimp. The anti-lipopolysaccharide factor type 3 (ALFPm3) gene, previously reported in P. monodon (Supungul et al., 2002) was found among the up-regulated genes but diversity due to amino acid changes was observed. Increase in ALFPm3 transcripts upon V. harveyi injection is in accordance with that found in the previous study.

• BMB Reports
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• v.45 no.2
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• pp.96-101
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• 2012

Urea-based nitrogen fertilizer was widely utilized in maize production, but transporters involved in urea uptake, translocation and cellular homeostasis have not been identified. Here, we isolated three maize aquapoin genes, ZmNIP2;1, ZmNIP2;4 and ZmTIP4;4, from a cDNA library by heterogous complementation of a urea uptake-defective yeast. ZmNIP2;1 and ZmNIP2;4 belonged to the nodulin 26-like intrinsic proteins (NIPs) localized at plasma membrane, and ZmTIP4;4 belonged to the tonoplast intrinsic protein (TIPs) at vacuolar membrane. Quantitative RT-PCR revealed that ZmNIP2;1 was expressed constitutively in various organs while ZmNIP2;4 and ZmTIP4;4 transcripts were abundant in reproductive organs and roots. Expression of ZmTIP4;4 was significantly increased in roots and expanded leaves under nitrogen starvation, while those of ZmNIP2;1 and ZmNIP2;4 remained unaffected. Functions of maize aquapoin genes in urea transport together with their distinct expression manners suggested that they might play diverse roles on urea uptake and translocation, or equilibrating urea concentration across tonoplast.

• Journal of Plant Biotechnology
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• v.7 no.2
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• pp.87-95
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• 2005

The tomato ripening associated membrane protein (TRAMP) (Fray et al., 1994) is a member of the major intrinsic protein (MIP) family, defined as channels facilitating the passage of water and small solutes through membranes. During normal fruit ripening the TRAMP mRNA levels were increased whereas the expression levels of TRAMP in low ethylene ACO1-sense suppressed lines, Nr and rin fruits, were lower than at the breaker stage of wild type fruit. TRAMP mRNA is inhibited by $LaCl_3$, which is an inhibitor of $Ca^{2+}$-stimulated responses, treatment but drought condition did not affect TRAMP expression. The levels of TRAMP mRNA transcripts were substantially higher in the dark treated seedlings and fruits. These suggest that TRAMP function as a water channel may be doubted because of several reasons; no water content was changed during ripening in wild type, antisense and overexpression lines, TRAMP expression under light condition was lower than dark condition and TRAMP expression was not changed in drought condition. Co-suppression plant, 3588 was one of sense suppression lines, which contain CaMV 35S promoter and sense pNY507 cDNA, produced small antisense RNA, approximately 21-25 nucleotides in length, mediated post-transcriptional gene silencing. Therefore, TRAMP expression was inhibited by small antisense and multiple copies might induce gene silencing without any production of double strand RNA. Total seven selected volatile productions, isobutylthiazole, 6-methyl-5-hepten-2-one, hexanal, hexenal methylbutanal, hexenol, and methylbutanol, were highly reduced in sense line whereas total volatile production was increased in TRAMP antisense line. These results suggested TRAMP might change volatile related compounds.

• The Plant Pathology Journal
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• v.22 no.4
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• pp.353-359
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• 2006

Transgenic Nicotiana benthamiana plants harboring the coat protein(CP) gene of Zucchini green mottle mosaic virus(ZGMMV) were chosen as a model host for the environmental risk assessment of genetically modified plants with virus resistance. This study was focused on whether new virus type may arise during serial inoculation of one point CP mutant of ZGMMV on the transgenic plants. In vitro transcripts derived from the non-functional CP mutant were inoculated onto the virus-tolerant and -susceptible transgenic N. benthamiana plants. Any notable viral symptoms that could arise on the inoculated transgenic host plants were not detected, even though the inoculation experiment was repeated a total of ten times. This result suggests that potential risk associated with the CP-expressiing transgenic plants may not be significant. However, cautions must be taken as it does not guarantee environmental safety of these CP-mediated virus-resistant plants, considering the limited number of the transgenic plants tested in this study. Further study at a larger scale is needed to evaluate the environmental risk that might be associated with the CP-mediated virus resistant plant.

• The Plant Pathology Journal
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• v.33 no.6
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• pp.608-613
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• 2017

The full-length sequence of a new isolate of Apple chlorotic leaf spot virus (ACLSV) from Korea was divergent, but most closely related to the Japanese isolate A4, at 84% nucleotide identity. The full-length cDNA of the Korean isolate of ACLSV was cloned into a binary vector downstream of the bacteriophage T7 RNA promoter and the Cauliflower mosaic virus 35S promoter. Chenopodium quinoa was successfully infected using in vitro transcripts synthesized using the T7 promoter, detected at 20 days post inoculation (dpi), but did not produce obvious symptoms. Nicotiana occidentalis and C. quinoa were inoculated through agroinfiltration. At 32 dpi the infection rate was evaluated; no C. quinoa plants were infected by agroinfiltration, but infection of N. occidentalis was obtained.

• Journal of the Korean Society for Library and Information Science
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• v.47 no.3
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• pp.343-361
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• 2013

We proposed and evaluated a tag semantic analysis method in which original tags are expanded and the semantic relations between original or expanded tags are used to extract key sentences from lecture speech transcripts. To do that, we first investigated how useful Flickr tag clusters and WordNet synonyms are for expanding tags and for detecting the semantic relations between tags. Then, to evaluate our proposed method, we compared it with a latent semantic analysis (LSA) method. As a result, we found that Flick tag clusters are more effective than WordNet synonyms and that the F measure mean (0.27) of the tag semantic analysis method is higher than that of LSA method (0.22).

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 1986.12a
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• pp.505.1-505
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• 1986

The gene for iso-1-cytochrome c for Saccharomyces cerevisiae was recloned into a pSP65 vector containing an active bacteriophage SP6 promoter. The iso-1-cytochrome c gene was cloned as an 856 bp Xho 1-Hind III fragment. When the resulting plasmid was digested at the Hind 111 site 279 bases downstream from the termination codon of the gene and transcribed in vitro using SP6 RNA polymerase, full length transcripts were produced. The SP6 iso-1-cytochrome c mRNA was translated using a rabbit reticulocyte lysate system and the protein products analyzed on SDS polyacrylamide gels. One major band was detected by autofluorography. This band was found to have a molecular weight of 12,000 Da and coincided with the Coomassie staining band of apocytochrome c from S. cerebisiae. The product was also shown to be identical with that of standard yeast apocytochrome c on an isoelectric focusing gel. The in vitro synthesized iso-a-cytochrome c was methylated by adding partially purified S-adenosyl-L-methionine . protein-lysine N-methyltransferase (Protein methylase III; EC 2.1.1.43) from S. cerevisiae along with S-adenosyl-L-methionine to the in vitro translation mixtures. The methylation was shown to be inhibited by the addition of the methylase inhibitor S-adenosyl-L-homocysteine or the protein synthesis inhibitor pu omycin. The methyl derivatives in the protein were identified as $\varepsilon$-N-mono, di and trimethyllysine by amino acid analysis. The molar ratio of methyl groups incorporated to that of cytochrome c molecules synthesized showed that 23% of the translated cytochrome c molecules were methylated by protein methylase III.