• The Korean Journal of Mycology
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• v.26 no.4 s.87
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• pp.450-457
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• 1998

The cryparin of Cryphonectria parasitica belongs to a cell wall associated fungal hydrophobin. The cryparin, though it is encoded by a single copy gene, is known for the high expression during the liquid culture of C. parasitica, and it turns out that 22% of total mRNA was transcribed for cryparin at 48hr after the liquid culture. In addition, it is also known as one of down-regulated fungal proteins by the presence of double stranded RNA virus, Cryphonectria hypovirus 1. In previous studies (Kim et al., 1999), we have constructed a cryparin-null mutant by replacing the cryparin gene with hygromycin B resistance gene due to site directed homologous recombination. In order for the promoter analysis of cryparin which seems to be very strong as well as mycoviral specific, it is preferable to have a strain with only a target promoter replaced and a discernable target site for incoming vectors. However, the cryparin-null mutant revealed the presence of an additional copy of transforming vector except the one which replaced the cryparin gene. In addition, the cryparin-null mutant did not contain any markers for targeted integration of incoming vectors. This prompts us to design an experiment to obtain a strain for promoter analysis of cryparin gene. A different mating type strain EP6(Mata, $met^-$) was mated with the cryparin-null mutant ${\triangle}$Crp194-7(MatA, Crp${\triangle}$::hph) to make the progenies with only a single replacement vector and $met^-$ characteristic remained. Nutritional assay as well as Southern blot analysis revealed that the progeny, ${\triangle}$Crp194-a6, was the methionine auxotroph with a single replacing vector in genome. Northern blot analysis and PAGE showed that there was no cryparin produced in this bred strain either.

• Korean Journal of Head & Neck Oncology
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• v.25 no.1
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• pp.28-32
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• 2009

Background : The most frequently reported risk factors for head and neck suamous cell carcinoma are smoking and alcohol. But in a recent overview, human papilloma virus(HPV) infection was revealed the important carcinogenic factor in oropharyngeal cancer. We aimed to clarify whether HPV directly effects on the oncogenesis and biologic behavior of hean and neck squamous cell carcinoma by comparison with infection prevalence, and physical status of virus. Material and Method : We used HPV genotyping DNA chip(Biocore, Korea, Seoul) arrayed by multiple oligonucleotide probes of L1 sequence of 26 types of HPV and HPV genotypes are identified by fluorescence scanner. The copy numbers of HPV E2 and E6 open reading frames(ORF) were assessed using a TaqMan-based 5'-exonuclease quantitative real-time PCR assay. The ratio of E2 to E6 copy numbers was calculated to determine the physical status of HPV-16 viral gene. Results : We observed a significant difference in HPV prevalence between tonsillar cancer group and control group(73.1% vs. 11.6%), and most of the HPVs were type 16(87.2%) and integrated(94.1%) state. In terms of oral tongue cancer, we demonstrate that 30.5% has integrated HPV-16 in cancer tissue. But Glottic cancer only 1% is related to HPV-16 integration. Conclusion : This study revealed significant relationship of HPV prevalence with oropharyngeal and oral tongue squamous cell carcinoma. Most of HPV were 16 type and integrated or mixed, HPV-16 integration could be directly related to the carcinogenesis.

• Microbiology and Biotechnology Letters
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• v.38 no.1
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• pp.40-45
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• 2010

The gene encoding $\beta$-agarase (agaB) which hydrolyzes $\beta$-1,4 linkages of agarose from Zobellia galactanivorans was cloned and fused to Saccharomyces cerevisiae mating factor alpha-1 secretion signal ($MF{\alpha}1$), in which the transcription of $MF{\alpha}1$-AgaB was under the control of AOX1 (alcohol oxidase 1, methanol inducible) promoter. The constructed plasmid pPIC-AgaB (9 kb) was integrated into HIS4 gene locus of Pichia pastoris genome. Successful integration was confirmed by performing colony PCR. The transformed cells showed red halos around its colonies in methanol agar plate by adding iodine solution, indicating the active expression of agaB in P.pastoris. By SDS-PAGE and zymographic analysis, the molecular weight of $\beta$-agarase was estimated to be a 53 kDa and about 15% N-linked glycosylation was occurred. The activity of extracellular $\beta$-agarase reached 1.34, 1.42 and 1.53 units/mL by inducing 0.1, 0.5, and 1% methanol, respectively, at baffled flask culture of P.pastoris GS115/pPIC-AgaB for 48 hr. Most of the enzyme activity was found in the extacellular fraction and the secretion efficiency showed 98%. Thermostability of recombinant $\beta$-agarase was also increased by glycosylation.

• Journal of Life Science
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• v.22 no.12
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• pp.1614-1620
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• 2012

Transgenic rice plants with increased resistance to rice brown planthopper (Nilaparvata lugens St${\aa}$l) were generated by particle bombardment-mediated transformation of plants with a gene encoding snowdrop lectin (Galanthus nivalis agglutinin; GNA) under control of the rice Rubisco small subunit (rbcS) promoter.. A large number of transgenic rice plants containing the GNA gene were generated. The integration, expression, and inheritance of this gene in the $R_1$ and $R_2$ generations were demonstrated by Southern and western blot analyses. The plants contained one to five copies of the transgene. The GNA protein comprised approximately 0.01-2.0% of total soluble protein in the $R_1$ and $R_2$ transgenic plants. Insect bioassays and feeding studies showed that the GNA protein expressed in the $R_2$ transgenic rice plants reduced the survival of brown planthoppers. The introduction of GNA into rice plants therefore can help to control insect pests.

• Molecules and Cells
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• v.41 no.5
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• pp.413-422
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• 2018

Soybean transgenic plants with ectopically expressed AtABF3 were produced by Agrobacterium-mediated transformation and investigated the effects of AtABF3 expression on drought and salt tolerance. Stable Agrobacterium-mediated soybean transformation was carried based on the half-seed method (Paz et al. 2006). The integration of the transgene was confirmed from the genomic DNA of transformed soybean plants using PCR and the copy number of transgene was determined by Southern blotting using leaf samples from $T_2$ seedlings. In addition to genomic integration, the expression of the transgenes was analyzed by RT-PCR and most of the transgenic lines expressed the transgenes introduced. The chosen two transgenic lines (line #2 and #9) for further experiment showed the substantial drought stress tolerance by surviving even at the end of the 20-day of drought treatment. And the positive relationship between the levels of AtABF3 gene expression and drought-tolerance was confirmed by qRT-PCR and drought tolerance test. The stronger drought tolerance of transgenic lines seemed to be resulted from physiological changes. Transgenic lines #2 and #9 showed ion leakage at a significantly lower level (P < 0.01) than ${\underline{n}}on-{\underline{t}}ransgenic$ (NT) control. In addition, the chlorophyll contents of the leaves of transgenic lines were significantly higher (P < 0.01). The results indicated that their enhanced drought tolerance was due to the prevention of cell membrane damage and maintenance of chlorophyll content. Water loss by transpiration also slowly proceeded in transgenic plants. In microscopic observation, higher stomata closure was confirmed in transgenic lines. Especially, line #9 had 56% of completely closed stomata whereas only 16% were completely open. In subsequent salt tolerance test, the apparently enhanced salt tolerance of transgenic lines was measured in ion leakage rate and chlorophyll contents. Finally, the agronomic characteristics of ectopically expressed AtABF3 transgenic plants ($T_2$) compared to NT plants under regular watering (every 4 days) or low rate of watering condition (every 10 days) was investigated. When watered regularly, the plant height of drought-tolerant line (#9) was shorter than NT plants. However, under the drought condition, total seed weight of line #9 was significantly higher than in NT plants (P < 0.01). Moreover, the pods of NT plants showed severe withering, and most of the pods failed to set normal seeds. All the evidences in the study clearly suggested that overexpression of the AtABF3 gene conferred drought and salt tolerance in major crop soybean, especially under the growth condition of low watering.

• BMB Reports
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• v.44 no.2
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• pp.107-112
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• 2011

We have developed a biologist-friendly, stand-alone Java GUI application, IdBean, for ID conversion. Our tool integrated most of the widely used ID conversion services that provide programmatic access. It is the first GUI ID conversion application that supports the direct merging as well as comparison of conversion results from multiple ID conversion services without manual effort. This tool will greatly help biologists who handle multiple ID types for the analyses of gene or gene product lists. By referring to multiple conversion services, the number of failed IDs can be reduced. By accessing ID conversion service online, it will potentially provide the most up-to-date conversion results. The application was developed in modular form; however, it can be re-packaged into plug-in form. For the development of a bioinformatics analysis tool, the module can be used as a built-in ID conversion component. It is available at http://neon.gachon.ac.kr/IdBean/.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.147-154
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• 2003

Microarray information system is a complex system to manage, analyze and interpretate microarray gene expression data. Establishment of well-defined development process is very essential for understanding the complexity and organization of the system. We performed object-oriented analysis using Unified Modeling Language (UML) in specifying, visualizing and documenting microarray information system. The object-oriented analysis consists of three major steps: (i) use case modeling to describe various functionalities from the user's perspective (ii) dynamic modeling to illustrate behavioral aspects of the system (iii) object modeling to represent structural aspects of the system. As a result of our modeling activities we provide the UML diagrams showing various views of the microarray information system. We believe that the object-oriented analysis ensures effective documentations and communication of information system requirements. Another useful feature of object-oriented technique is structural continuity to standard microarray data model MAGE-OM (Microarray Gene Expression Object Model). The proposed modeling e(forts can be applicable for integration of biomedical information system.

• Journal of Plant Biotechnology
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• v.35 no.1
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• pp.41-45
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• 2008

Laccase (EC 1.10.3.2) is a small group of enzymes that catalyze the oxidation of a broad range of phenolic compounds including hazardous and recalcitrant pollutants in the environment. This study attempted to develop an efficient system for production of a recombinant laccase by chloroplast genetic transformation of tobacco. Chloroplast transformation vector was constructed and introduced into the tobacco chloroplast genome using particle bombardment. Chloroplast-transformed plants were subsequently regenerated. PCR and southern blot analyses confirmed stable integration of the laccase gene into the chloroplast genome. Northern blot analysis revealed that mRNA of the laccase gene was highly expressed in chloroplast-transformed plants.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.114-114
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• 2017

The aim of this research is to improve Korean lettuce varieties in terms of Fusarium wilt, bolting under hot weather and nutritional function applying genomics approaches. To find related gene/molecular markers, we selected 96 lettuce varieties which are popular in domestic fresh vegetable markets. To construct frame works of the genomic approaches, we exploited GBS(Genotyping by Sequencing) and found total 61,407 SNPs from lettuce whole genomes (MAF>0.02). We observed that Three SNPs array per 100kb of lettuce genome. Average LD decay is expected to expand up to 3.9M(million)bp. Thus, we concluded that about 104 SNPs exist within a LD, which is sufficient to use GWAS(Genome-wide Association Study) to explore the useful gene/molecular markers. In addition, we optimized mass screening method to evaluate disease resistance levels against Fusarium wilt and are testing the bolting sensitivity during summer growing season for those lettuce allele mining set.

• Journal of Plant Biotechnology
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• v.40 no.1
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• pp.49-54
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• 2013

C3HC4-type RING zinc finger proteins essential in the regulation of plant processes, including responses to abiotic stresses. We previously isolated and examined the C3HC4-type RING zinc finger protein (BrRZFP1) from Brassica rapa under abiotic stresses. To elucidate the role of the BrRZFP1 transcription factor in gene regulation, we transformed tobacco plants with the BrRZFP1 gene. Plants were regenerated from 82 independently transformed callus lines of tobacco and analysed for transgene expression. Transgene integration and expression was confirmed by Southern and RT-PCR analyses, respectively. T2 plants displayed more tolerance to the bacterial pathogens Pectobacterium carotovorum and Ralstonia solanacearum, and the tolerance levels were correlated with BrRZFP1 expression levels. These results suggest that the transcription factor BrRZFP1 is an important determinant of stress response in plants and its overexpression in plants could increase biotic stress resistance.