• Korean Journal of Plant Tissue Culture
• /
• v.25 no.1
• /
• pp.45-50
• /
• 1998

Hypocotyl explants of flowering cabbage were precultured on MS medium without kanamycin and then cocultured with Agrobacterium tumefaciens LBA4404;;pGA875 harboring insect resistantce proteinase inhibitor II(PI-II) gene in MS liquid medium adjusted pH 5.5 for 72hr. These explants were transferred to MS medium containing 20 mg/L kanamycin, 500 mg/L carbenicillin, and 1 mg/L BA. The explants were subsequently subcultured every 2 weeks. After 4 weeks of subculture, kanamycin-resistant shoots were obtained from selection medium. Leaves of putative transformants survived on MS selection medium containing 30 mg/L kanamycin. Incoporation of the PI-II gene into flowering cabbage was confirmed by PCR analysis of genomic DNA. Southern blot analysis showed that ECL-labeled probe for PI-II gene was hybridized to the expected amplified genomic DNA fragment of about 500 by from transgenic flowering cabbage.

• Journal of Plant Biotechnology
• /
• v.41 no.1
• /
• pp.50-55
• /
• 2014

Plant-based vaccines possess some advantages over other types of vaccine biotechnology such as safety, low cost of mass vaccination programs, and wider use of vaccines for medicine. This study was undertaken to develop the transgenic maize as edible vaccine candidates for humans. The immature embryos of HiII genotype were inoculated with A. tumefaciens strain C58C1 containing the binary vectors (V662 or V663). The vectors carrying nptII gene as selection marker and scEDIII (V662) or wCTB-scEDIII (V663) target gene, which code EIII proteins inhibite viral adsorption by cells. In total, 721 maize immature embryos were transformed and twenty-two putative transgenic plants were regenerated after 12 weeks selection regime. Of them, two- and six-plants were proved to be integrated with scEDIII and wCTB-scEDIII genes, respectively, by Southern blot analysis. However, only one plant (V662-29-3864) can express the gene of interest confirmed by Northern blot analysis. These results demonstrated that this plant could be used as a candidated source of the vaccine production.

• Plant Biotechnology Reports
• /
• v.2 no.1
• /
• pp.47-58
• /
• 2008

To select agronomically useful transgenic plants, a large number of transgenic events are initially produced, gene transfer confirmed, and advanced to obtain homozygous lines for testing in field trials. Direct in planta assays for identifying the transgene carriers in the segregating progeny are based on the activity of selectable marker gene and are easy, simple and inexpensive. For this purpose, expression of bar gene as measured by tolerance to damage by glufosinate ammonium, the active ingredient in the herbicide BASTA, was investigated. Dose damage curves were generated by leaf paint tests with BASTA on four genotypes of sorghum. Transgenic plants were characterized in terms of sensitivity to the concentration of glufosinate ammonium. In transgenics, symptoms of BASTA swab tests at different growth stages and PCR analysis for cry1B were carried out and correlated. Germination tests could not be employed for large scale evaluation of transgenic progeny because of mortality of tolerant seedlings after transplantation to soil. Based on the above findings, a simple, inexpensive, time-saving, two-step scheme for effective evaluation of transgenics and their progeny containing bar gene as selection marker using BASTA swab tests is described.

• The Korean Journal of Applied Statistics
• /
• v.29 no.4
• /
• pp.643-656
• /
• 2016

High dimensional data are frequently encountered in various fields where the number of variables is greater than the number of samples. It is usually necessary to select variables to estimate regression coefficients and avoid overfitting in high dimensional data. A penalized regression model simultaneously obtains variable selection and estimation of coefficients which makes them frequently used for high dimensional data. However, the penalized regression model also needs to select the optimal model by choosing a tuning parameter based on the model selection criterion. This study deals with the bias effect of LASSO regression for model selection criteria. We numerically describes the bias effect to the model selection criteria and apply the proposed correction to the identification of biomarkers for lung cancer based on gene expression data.

• Molecules and Cells
• /
• v.23 no.2
• /
• pp.192-197
• /
• 2007

Bulb color in onions (Allium cepa) is an important trait whose complex inheritance mechanism involves epistatic interactions among major color-related loci. Recent studies revealed that inactivation of dihydroflavonol 4-reductase (DFR) in the anthocyanin synthesis pathway was responsible for the color differences between yellow and red onions, and two recessive alleles of the anthocyanidin synthase (ANS) gene were responsible for a pink bulb color. Based on mutations in the recessive alleles of these two genes, PCR-based markers for allelic selection were developed. In this study, genotype analysis of onions from segregating populations was carried out using these PCR-based markers. Segregating populations were derived from the cross between yellow and red onions. Five yellow and thirteen pink bulbs from one segregating breeding line were genotyped for the two genes. Four pink bulbs were heterozygous for the DFR gene, which explains the continuous segregation of yellow and pink colors in this line. Most pink onions were homozygous recessive for the ANS gene, except for two heterozygotes. This finding indicated that the homozygous recessive ANS gene was primarily responsible for the pink color in this line. The two pink onions, heterozygous for the ANS gene, were also heterozygous for the DFR gene, which indicated that the pink color was produced by incomplete dominance of a red color gene over that of yellow. One pink line and six other segregating breeding lines were also analyzed. The genotyping results matched perfectly with phenotypic color segregation.

• Molecular & Cellular Toxicology
• /
• v.2 no.1
• /
• pp.7-10
• /
• 2006

We performed comprehensive SNP validation and linkage disequilibrium (LD) analysis of the c-fos induced growth factor (Figf) gene in Korean population. Out of 32 SNPs, only 9 SNPs were polymorphic in Korean population. Validated SNPs formed a single extended haplotype block with strong LD through the entire length of the gene. Tagging SNP analysis picked only 2 SNPs to represent most of the genetic variation information of the Figf gene. Our results demonstrate the utility of LD block and tagging SNP analysis for an efficient way of performing a candidate gene based association study.

• Genomics & Informatics
• /
• v.18 no.4
• /
• pp.41.1-41.8
• /
• 2020

We provide an algorithm for the construction and analysis of autocorrelation (information) functions of gene nucleotide sequences. As a measure of correlation between discrete random variables, we use normalized mutual information. The information functions are indicative of the degree of structuredness of gene sequences. We construct the information functions for selected gene sequences. We find a significant difference between information functions of genes of different types. We hypothesize that the features of information functions of gene nucleotide sequences are related to phenotypes of these genes.

• The Plant Pathology Journal
• /
• v.30 no.2
• /
• pp.195-199
• /
• 2014

Apple stem pitting virus (ASPV), of the Foveavirus genus in the family Betaflexiviridae, is one of the most common viruses of apple and pear trees. To examine variability of the coat protein (CP) gene from ASPV, eight isolates originating from 251 apple trees, which were collected from 22 apple orchards located in intensive apple growing areas of the North Gyeongsang and North Jeolla Provinces in Korea, were sequenced and compared. The nucleotide sequence identity of the CP gene of eight ASPV isolates ranged from 77.0 to 97.0%, while the amino acid sequence identity ranged from 87.7 to 98.5%. The N-terminal region of the viral CP gene was highly variable, whereas the C-terminal region was conserved. Genetic algorithm recombination detection (GARD) and single breakpoint recombination (SBP) analyses identified base substitutions between eight ASPV isolates at positions 54 and 57 and position 771, respectively. GABranch analysis was used to determine whether the eight isolates evolved due to positive selection. All values in the GABranch analysis showed a ratio of substitution rates at non-synonymous and synonymous sites (dNS/dS) below 1, suggestive of strong negative selection forces during ASPV CP history. Although negative selection dominated CP evolution in the eight ASPV isolates, SLAC and FEL tests identified four possible positive selection sites at codons 10, 22, 102, and 158. This is the first study of the ASPV genome in Korea.

• Korean Journal of Plant Resources
• /
• v.17 no.1
• /
• pp.28-33
• /
• 2004

This study was conducted to simple transformants selection by herbicide Basta treatment after transformation with Agrobacteium tumefaciens MP90/PAT in hybrid poplar(Populus alba ${\times}$ P. glandulosa No. 3). In preliminary study, we determined that the lethal concentration of herbicide Basta was 1.0mg/L in callus culture, adventitious bud formation and axillary bud elongation experiment. By the treatment of 1.0mg/L Basta, we could be selected the transformed shoots effectively from the various cultures. In addition, the treatment was useful on selection of transformants which are growing in soil pot. Finally, we also confirmed the transformation by PAT assay, Above results show that the herbicide Basta treatment and PAT assay can be a very simple and effective method for the identification of PAT gene transformed hybrid poplar.

• Journal of Plant Biotechnology
• /
• v.2 no.2
• /
• pp.89-96
• /
• 2000

For large DNA fragment transformation in dicots and monocots, BIBAC2 vector system was applied to Arabidopsis thaliana and Oryza sativa L. cv. Jinmi as a model plant, respectively. For Arabidopsis, the Th1 gene in T23L3 BAC clone whose size is about 90 kb was used as the target gene source for transformation. Because T23L3 BAC clone was originally constructed in pBelloBAC11, the target gene was reconstructed into BIBAC2. As the results of reconstruction, 476 colonies were survived in selection medium containing 40 mg/L kanamycin. In colony hybridization analysis, 24 out of 476 colonies exhibited positive signals. In the pulsed-field gel electrophoresis analysis, 11 out of 24 positive clones exhibited the band at the location of 90 kb. In Southern hybridization, positive signal band at the location of 90 kb was observed in all 11 transformants. Using these verified clones, Agrobacterium-mediated transformation was applied to Arabidopsis thaliana th1-201 mutant for genetic complementation test. Twelve thousands T$_1$ seeds were harvested, and antibiotic selection test is being analyzed to verify whether these seeds were transformed. for rice, COR356 that contains 150 kb human genomic DNA in a BIBAC2 vector was used as the target gene. As the results of transformation, 151 out of 210 co-cultivated calli were survived in selection medium containing 5 mg/L hygromycin, and 45 out of 151 survived calli were regenerated into plants. Transformation efficiency was 21.6%. Progeny test using 71 seeds is being analyzed now. These results provide the potential that large DNA fragments can be transferred into both dicots and monocot by Agrobacterium-mediate d transformation system.