• Molecules and Cells
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• v.19 no.3
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• pp.318-327
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• 2005

Southern blot analysis revealed a ubiquitous distribution and high copy number of Ty3-gypsy-like elements in the genome of Hibiscus syriacus. Comparative phylogenetic analysis of the large subunit of Rubisco and the integrase region of Ty3-gypsy elements in various plant species indicated that the retrotransposon-like sequences have different evolutionary histories and their own unique polymorphism in the H. syriacus population. Sequence-tagged site-restriction fragment length polymorphisms (STS-RFLP) analysis also indicated great variability in the numbers and sequences of Ty3-gypsy-like elements within H. syriacus varieties. Ty3-gypsy-like elements may still be active within H. syriacus, since Northern analysis of wounded leaves of H. syriacus variety Saehan with a probe for the integrase domain gave strong hybridization signals. The sequence heterogeneity and ubiquity of the Ty3-gypsy-like elements in H. syriacus genomes could provide reliable DNA markers for line identification as well for the analysis of genetic diversity in H. syriacus.

• Journal of Genetic Medicine
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• v.2 no.1
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• pp.23-26
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• 1998

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder which has been clinically shown to cause progressive weakness and result in atrophy of the facial muscles, shoulder girdle and upper arm muscles. The responsible gene for the FSHD has been located on chromosome 4q35-qter. The probes p13E-11 and pFR-1 detect DNA rearrangements associated with FSHD as under 28 kb DNA fragment in genomic southern analysis digested with EcoRI and the fragment contains 3.3 kb Kpn I tandem repeats. In this study, 4 fetuses with a family history of FSHD were analysed by genomic southern hybridization analysis with probes to determine whether they carried the deleted region. Of the 4 fetuses, three of them had mothers who were FSHD patients and the other one had a father affected with FSHD. After 10-11 weeks of gestation, we performed chorionic villi sampling and extracted DNA from uncultured and cultured tissue cells for the direct DNA analysis. The result of the southern analysis showed two fetuses having received about 15-18 kb of deleted genes from the father and the mother respectively, and found to be FSHD patients. The other two fetuses were shown to have two normal alleles from the parents and found to be normal. Two pregnancies which were determined to be normal were carried to term delivering two healthy babies.

• Journal of the korean academy of Pediatric Dentistry
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• v.25 no.2
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• pp.292-303
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• 1998

The arbitrary primer polymerase chain reaction(AP-PCR) and Southern blot restriction fragment length polymorphism(RFLP) were used to genotype the cariogenic pathogen S. mutans in children. Following the morphologic chracteristics of colony on selective medium for S. mutans, total genomic DNA from 155 strains was extracted by conventional methods. Among 155 strains, 143 strains (92.3%) were confirmed S. mutans by PCR with dexA gene and 114 strains were used in this study. Three random sequence 10-base oligonucleotide primers were chosen for AP-PCR. The amplified DNA products were separated electrophoretically in a 2% agarose gel containing ethidium bromide and the banding patterns were compared among different strains. For RFLP analysis, DNA was digested with EcoRI and BamHI, separated on a 0.7 % agarose gel and transferred to a nylon membrane. The membrane was probed with a previously characterised 1.6 kilobases (kb) DNA fragment cloned from gtf B gene of S. mutans. The probe was labeled with isotope[$^{32}P-{\alpha}CTP$], and hybridized fragments were detected with intensifying screen. AP-PCR produced 4-8 DNA bands in the 0.25-10 kb regions and distinguished 9, 10 or 12 genotypes, depending on the specific primer used. Southern blot RFLP analysis revealed 2 hybridization patterns consisting of 1 DNA fragments 450, 500 bp. These results indicate that AP-PCR is more discriminative method for genotyping of S. mutans.

• Journal of Microbiology and Biotechnology
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• v.20 no.6
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• pp.1027-1031
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• 2010

To examine the possibility of horizontal gene transfer between transgenic potatoes and microorganisms in potato fields, the gene flow from transgenic potatoes containing the nucleoside diphosphate kinase 2 (NDPK2) gene to microorganisms in soils was investigated. The soil samples collected from the potato fields from March to October 2007 were examined by PCR, Southern hybridization, and AFLP fingerprinting. The NDPK2 gene from soil genomic DNAs was not detected by both PCR and Southern hybridization, indicating that gene transfer did not occur in the potato fields. In addition, no discrepancy was found in pathogenicity and noticeable changes for the appearance of variants of Phytophthora infestans in each generation when serial inoculations and the analysis of genomic DNAs by AFLP were conducted. Thus, these data suggest that transgenic potatoes do not give significant impacts on the communities of soil microorganisms and the emergence of variants, although continued research efforts may be necessary to make a decisive conclusion.

• Journal of The Korean Society of Grassland and Forage Science
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• v.26 no.2
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• pp.83-90
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• 2006

To develop transgenic birdsfoot trefoil (Lotus corniculatus L.) plants tolerant to environmental stress, Arabidopsis NDPK gene (AtNDPK) was introduced into birdsfoot trefoil plants using Agrobacterium-mediated transformation and expressed powerfully under the control of the E35S promoter. The expression vector, pEN-K was used for introduction of AtNDPK gene into birdsfoot trefoil plaits. The transformed calli were selected on kanamycin containing medium and then regenerated. The transformed birdsfoot trefoil plants were cultivated for 4 months on BOi2Y medium. Genomic DNA PCR and Southern blot analysis confirmed the incorporation of AtNDPK into the birdsfoot trefoil genome.

• Korean journal of applied entomology
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• v.38 no.2
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• pp.145-149
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• 1999

To develop the baculovirus expression vector system (BEVS) adopting p10 gene promoter of Spodoptera exigua nucleopolyhedrovirus (SeNPV), we characterized the p10 gene of SeNPV. The nucleotide sequence of 545 bases including the coding region of p10 gene was determined. Compared with the previously reported SeNPV p10 gene (Zuidema et al., 1993), 4 bases were different in the 5' and 3' flanking region but no difference was found in the coding region. The p10 gene was located within Xho I 1.5 Kb, Sph 1 2.4 Kb and Cla I 4.0 Kb fragments by Southern hybridization analysis. Also, the Sph I 2.4 Kb and the Cla I 4.0 Kb fragments were cloned and their restriction enzyme maps were determined.

• The Korean Journal of Mycology
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• v.17 no.4
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• pp.209-213
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• 1989

Transformation of an auxotrophic requirement for uracil in Pleurotus florida P101 has been achieved using chimeric vector containing Aspergillus nidulans ans 1, and Neurospora crassa pyr 4 DNA. Protoplasts of $Ura^-$strains of P. florida were incubated with plasmid pDJB3 containing the cloned pyr 4 gene in the presence of polyethylene glycol and $CaCl_2$. Transformants could grow on MMM showing mitotical stability. Southern hybridization analysis of DNA isolated from transformants showed that the Neurospora pyr 4 gene and vector sequence might be integrated into the P. florida chromosomes. As the transformants were monokaryon, each transformant was mated with the other monokaryon. Fruitbody shape of untransformant was eroded type but those of transformants were eroded type, funnel type, plane type and ungrowing cap type.

• Journal of Life Science
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• v.5 no.3
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• pp.105-116
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• 1995

To investigate genomic changes in c-myc gene by a chemical carcinogen, human lymphoblast NC-37 cells were exposed to benzo(a)pyrene(BP) and dimethylbenzanthracene(DMBA), and the c-myc gene expression was evaluated by Northern and Southern blot hybridization techniques. The results are as follows: When the genomic DNA of NC-37 cells exposed to several concentrations(1.25, 2.5 and 5ug/ml) of BP concentration. However, the c-myc gene was most significantly enhanced with 2.5ug/ml of BP. The expressions of c-myc gene in NC-37 cells was stimulated by BP and DMBA. Addition of TPA reduced the gene expression BP-treated cells, whereas it enhanced the gene expression in DMBA-treated cells. The expression of c-H-ras gene was slightly increased by treatment with BP and DMBA alone and in combination with TPA, however the magnitude of increase was not significantly different between each other. The expressions of c-myc c-H-ras genes in Burkitt's lymphoma cells were greater than those in NC-37 cells. When the DNA extracted from NC-37 cells exposed to various concentrations of BP were amplified by polymerase chain reaction using a primer set containing c-myc exon I, the amplified products were of the same size in all groups. To evaluate the BP toxicity in E.coli to which human c-myc gene-cloned pBR322 vector was inserted, Southern blot hybridization was conducted on c-myc genes digested with EcoRI/HindIII and Smal/Xbal restriction enzymes, and observing that in 2 ug/ml BP-treated cells a 3.5kb fragment was generated in addition to 1.3kb fragment which can be observed in normal cells. Direct nucleotide sequence analysis of polymerase chain reaction products showed a mutation of G$\longrightarrow$A transition at the Smal recognition site.

• Journal of Photoscience
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• v.12 no.2
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• pp.75-82
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• 2005

Rumex acetosa L. is a dioecious flowering plant with well developed sex chromosome system: 2n = 12 + XX in the female plants and 2n = 12 + XY1Y2 in the male plants. To isolate sex-linked DNA, we carried out chromosome micromanipulation, followed by DOP-PCR, AFLP of the PCR products, reverse Southern hybridization and sequence analysis. From 500 AFLP specific clones, 13 X-chromosome and 5 Y-chromosome specific clones were obtained. Except one clone RADAX-239 ($\underline{R}umex\;\underline{a}-\underline{D}OP-PCR-\underline{A}FLP-\underline{Y}-chromosome\;specific$), all clones appear to be R. acetosa plant-specific sequences and non-coding sequences. Southern blot analysis using these clones could not discriminate genomic DNAs either from male or female plants. Results of this study imply that both autosome-origin and degeneration of sex chromosomes are prevalent in plant systems.

• Molecules and Cells
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• v.23 no.2
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• pp.145-153
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• 2007

Elucidation of the roles of circadian associated factors requires a better understanding of the molecular mechanisms of circadian rhythms, control of flowering time through photoperiodic pathways, and photosensory signal transduction. In Arabidopsis, the APRR1 quintet, APRRs 1, 3, 5, 7, and 9, are known as central oscillator genes. Other plants may share the molecular mechanism underlying the circadian rhythm. To identify and characterize these circadian response genes in Brassica crops whose genome was triplicated after divergence from Arabidopsis, we identified B. rapa BAC clones containing these genes by BLAST analysis of B. rapa BAC end sequences against the five corresponding Arabidopsis regions. Subsequent fingerprinting, Southern hybridization, and PCR allowed identification of five BAC clones, one for each of the five circadian-related genes. By draft shotgun sequencing of the BAC clones, we identified the complete gene sequences and cloned the five expressed B. rapa circadian-associated gene members, BrPRRs 1, 3, 5, 7, and 9. Phylogenetic analysis revealed that each BrPRR was orthologous to the corresponding APRR at the sequence level. Northern hybridization revealed that the five genes were transcribed at distinct points in the 24 hour period, and Southern hybridization revealed that they are present in 2, 1, 2, 2, and 1 copies, respectively in the B. rapa genome, which was triplicated and then diploidized during the last 15 million years.