• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.339-343
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• 2005

Boolean networks(BN) construction is one of the commonly used methods for building gene networks from time series microarray data. However, BN has two major drawbacks. First, it requires heavy computing times. Second, the binary transformation of the microarray data may cause a loss of information. This paper propose two methods using liner regression to construct gene regulatory networks. The first proposed method uses regression based BN variable selection method, which reduces the computing time significantly in the BN construction. The second method is the regression based network method that can flexibly incorporate the interaction of the genes using continuous gene expression data. We construct the network structure from the simulated data to compare the computing times between Boolean networks and the proposed method. The regression based network method is evaluated using a microarray data of cell cycle in Caulobacter crescentus.

• Korean Journal of Microbiology
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• v.31 no.2
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• pp.136-140
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• 1993

The A. nidulans expression vector which contained trpC marker gene from A. nidulans was constructed to produce glucoamy]ase. The recombinant plasmid was introduced into auxotrophic mutant A. nidulans B17. Southern blot analysis of the genomic DNA from transformant showed that pKHG2 DNA had integrated into the A. nidulans chromosomes. Northern analysis of the total RNA from transform ant showed that mRNA of glucoamylase gene was synthesized in induction condition. Specific activity of glucoamylase was increased in transform ants. G]ucoamylase was shown to be active in non-denaturing acrylamide gel.

• BMB Reports
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• v.45 no.4
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• pp.207-212
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• 2012

Retroviruses have often been used for gene therapy because of their capacity for the long-term expression of transgenes via stable integration into the host genome. However, retroviral integration can also result in the transformation of normal cells into cancer cells, as demonstrated by the incidence of leukemia in a recent retroviral gene therapy trial in Europe. This unfortunate outcome has led to the rapid initiation of studies examining various biological and pathological aspects of retroviral integration. This review summarizes recent findings from these studies, including the global integration patterns of various types of retroviruses, viral and cellular determinants of integration, implications of integration for gene therapy and retrovirus-mediated infectious diseases, and strategies to shift integration to safe host genomic loci. A more comprehensive and mechanistic understanding of retroviral integration processes will eventually make it possible to generate safer retroviral vector platforms in the near future.

• Plant Resources
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• v.4 no.1
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• pp.26-30
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• 2001

To improve the iron content of red pepper, we have transferred the entire coding sequence of the ferritin gene(Fpl) into Capsicum annuum (L. cv. Chungyang and Bukang) by Agrobacterium mediated transformation. Transformants were found to contain the Fp1 gene at up to three loci, increased distinct iron content changes. In transgenic plants, iron content was as much as 7-fold to 8-folds greater than that of their untransformed counterparts. Furthermore, the Rl progenies from transformant(A7, A8) co-segregated into a 15:1 ratio for both Kanamycin resistance and genotype of high iron.

• Microbiology and Biotechnology Letters
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• v.25 no.1
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• pp.30-36
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• 1997

To genetically breed powerful multifunctional antagonistic bacteria, the urease gene of alkalophilic Bacillus pasteurii was transferred into Bacillus subtilis YB-70 which had been selected as a powerful biocontrol agent against root-rotting fungus Fusarium solani. Urease gene was inserted into the HindIII site of pGB215-110 and designated pGU266. The plasmid pGU266 containing urease gene was introduced into the B. subtilis YB-70 by alkali cation transformation system and the urease gene was very stably expressed in the transformant of B. subtilis YB-70(pGU266). The optimal conditions for the transfomation were also evaluated. From the in vitro antibiosis tests against F. solani, the antifungal activity of B. subtilis YB-70 containing urease gene was much efficient than that of the non-transformed strain. Genetic improvement of B. subtilis YB-70 by transfer of urease gene for the efficient control seemed to be responsible for enhanced plant growth and biocontrol efficacy by combining its astibiotic action and ammonia producing ability.

• Plant Biotechnology Reports
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• v.2 no.3
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• pp.199-206
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• 2008

We have developed an efficient system of assessing the ability of a gene silencing cassette to silence transcripts from recalcitrant or poorly studied plant species by using a model plant as a host for the gene of interest. Tobacco plants transgenic for Lachrymatory Factor Synthase (LFS) enzyme activity from onion were first produced by introducing a CaMV 35S-onion-lfs gene construct. These plants were then subjected to a second transformation with an RNAi construct directed against the lfs gene sequence. LFS enzyme activity assay showed that the transgenic plants, containing both the lfs gene and the RNAi construct, had significantly reduced LFS activity. This observation was supported by Western analysis for the LFS protein and further validated by quantitative RT-PCR analysis that demonstrated a significant reduction in the lfs transcript level in the dual transformants. In this work, we have demonstrated that the RNAi construct is a suitable candidate for the development of a non-lachrymatory onion. Our model plant RNAi system has wide-reaching applications for assessment and targeting of plant secondary pathway genes, from poorly studied or recalcitrant plant species, that are important in the pharmacological, food and process industries.

• The Plant Pathology Journal
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• v.32 no.3
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• pp.173-181
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• 2016

Gene disruption by homologous recombination is widely used to investigate and analyze the function of genes in Fusarium fujikuroi, a fungus that causes bakanae disease and root rot symptoms in rice. To generate gene deletion constructs, the use of conventional cloning methods, which rely on restriction enzymes and ligases, has had limited success due to a lack of unique restriction enzyme sites. Although strategies that avoid the use of restriction enzymes have been employed to overcome this issue, these methods require complicated PCR steps or are frequently inefficient. Here, we introduce a cloning system that utilizes multi-fragment assembly by In-Fusion to generate a gene disruption construct. This method utilizes DNA fragment fusion and requires only one PCR step and one reaction for construction. Using this strategy, a gene disruption construct for Fusarium cyclin C1 (FCC1), which is associated with fumonisin B1 bio-synthesis, was successfully created and used for fungal transformation. In vivo and in vitro experiments using confirmed fcc1 mutants suggest that fumonisin production is closely related to disease symptoms exhibited by F. fujikuroi strain B14. Taken together, this multi-fragment assembly method represents a simpler and a more convenient process for targeted gene disruption in fungi.

• Korean Journal of Plant Tissue Culture
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• v.24 no.1
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• pp.37-41
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• 1997

The in vitro regeneration and genetic transformation systems in hot pepper(Capsicum annuum L.) have not been routinely available, which has been a major limiting factor in the application of new genetic manipulations. An efficient procedure to regenerate whole pepper plants and to generate transgenic plants expressing a foreign gene was established. A relatively high frequency of plant regeneration was observed when hypocotyl and cotyledon explants were cultured on MS medium supplemented with NAA 0.1 mg/L plus zeatin 2.0 mg/L or IBA 10.0 mg/L plus BAP 1.0 mg/L. Addition of AgNO$_3$5 $\mu$M to these media improved the regeneration frequency up to 8%. For plant transformation, hypocotyl and cotyledon explants of hot pepper were precultured on shoot induction media without kanamycin added for 2 days, and then cocultured with Agrobacterium tumefaciens pDY183 for 2 days. Putative transformants were obtained from selection media containing 100 mg/L kanamycin sulfate and 500 mg/L carbenicillin. Putatively selected transformants were confirmed by amplification of selectable marker genes (ADA and NPT II) by polymerase chain reacion. Successful transcripts of ADA gene were detected by Northern blot analysis. Enzyme activity of ADA was also examined by spectrophotometric analysis, and expression of ADA gene in hot pepper suggests the potential application of ADA gene as a selectable marker in plants.

• Journal of Plant Biotechnology
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• v.30 no.1
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• pp.27-33
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• 2003

The optimal condition of in vitro regeneration and transformation were investigated for newly bred potato varieties in Korea. Leaf and internodal stem tissues of 'Chubak', 'Namsuh', 'Jasim', 'Jopung' and 'Jowon' were used to investigate the influence of growth regulator on regeneration efficiency The effect of phenolic compound acetosyringone on gene transformation efficiency was also investigated. Leaf tissue of 'Jowon' and internodal stem tissues of 'Jopung' were showed high regeneration efficiency on M5 medium supplemented with 0.1 mg/L GA₃, 2.0 mg/L Zeatin and 0.01 mg/L NAA. The other three potato cultivars were showed low regeneration efficiency less than 25%. The effect of acetosyringone on Agrobacterium-mediated gene transformation with leaf and internodal stem tissues were noticeable. By adding the 75 μM of acetosyringone during the Agrobacterium innoculation, the transformation efficiency was increased up to 1.5∼4.0 fold compare to non-treated control. In case of 'Jowon' the transformation efficiency was 87.9% in leaf tissue and 'Jopung' was 68.4% in internodal stem tissues.

• KSBB Journal
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• v.24 no.3
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• pp.279-286
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• 2009

Streptomyces is well known for their ability to synthesize enormous varieties of antibiotics as secondary metabolites. Among them, S. avermitilis produces avermectins, a group of antiparasitic agents used in human and veterinary medicine. However, S. avermitilis also produces oligomycin, which is a potential toxic inhibitor of oxidative phosphorylation in mammalian cells. Therefore, we decided to disrupt oligomycin synthetase gene to prevent co-production of oligomycin in S. avermitilis. To create plasmid for disruption, the smallest gene of oligomycin synthetase gene cluster was obtained by PCR from S. avermitilis chromosome. Then, apramycin resistance gene was inserted in oligomycin synthetase gene for selection. After transformation of this plasmid, oligomycin synthetase gene (olmA5) in the chromosome was displaced with disruption cassette on the plasmid via homologous recombination. As a result of this gene replacement, we obtained mutants (olmA5::apra) that no longer makes the toxic oligomycin. And the mutants confirmed by PCR and HPLC analysis. However, showed no increasement of avermectin production in the mutant was observed.