• Journal of Animal Science and Technology
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• v.50 no.6
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• pp.753-762
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• 2008

The primers for RT-PCR and RACE-PCR were designed by aligning the pig genomic sequence and the human complement factor B(CFB) coding sequence(CDS) from the GenBank. Each PCR product was amplified in pig cDNA and sequencing was carried out. The CDS length of pig CFB gene was determined to be 2298 bp. In addition, the pig CDS was more longer than human and mouse orthologs because of insertion and deletion. The identities of porcine nucleotide sequences with those of human and mice were 84% and 80%, and the identities of amino acids were 79% to 77%, respectively. Three complement control protein(CCP) domains, one Von Willebrand factor A(VWFA) domain and a serine protease domain, that are revealed typically in mammals, were found in the pig CFB gene. Based on the CDSs determined, the primers were designed in intron regions for amplification of entire length of exons. In amplification and direct sequencing with genomic DNAs of six pig breeds, three cSNPs(coding single nucleotide polymorphisms) were identified and verified as missense mutations. Using the Multiplex-ARMS method, we genotyped and verified the mutations identified from direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS with two randomly selected DNA samples. The genotype of each sample exhibited the same results using both methods. Therefore, three cSNPs were identified from pig CFB gene and that can be used for haplotype analysis of the swine leukocyte antigen(SLA) class III region. Moreover, the results indicate that the Multiplex-ARMS method should be powerful for genotyping of genes in the SLA region.

• Journal of Animal Science and Technology
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• v.49 no.5
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• pp.549-558
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• 2007

C4B and BAT2, assigned to the SLA class III region, were recently reported on relation with human diseases. The primers for RT-PCR and RACE-PCR for CDS analysis of these genes of pig were designed by aligning the CDSs of humans and mice from GenBank. After we amplified and sequenced with these primers and cDNAs, the full-length CDSs of pig were determined. The CDS lengths of C4B and BAT2 were shown as 5226 bp and 6501 bp. In addition, the identities of nucleotide sequences with human and mouse were 76% to 87%, and the identities of amino acids were 72% to 90%. After we carried out the alignment with determined CDSs in this study and pig genomic sequences from GenBank, the primers for cSNP detection in genome were designed in intron regions that flanked one or more exons. Then, we amplified and directly sequenced with genomic DNAs of six pig breeds. Four cSNPs from C4B and three 3 cSNPs from BAT2 were identified. In addition, amino acid substitution occurred in six cSNP positions except for C4248T of C4B. By the Multiplex-ARMS method, we genotyped seven cSNPs with DNA samples used for direct sequencing. We verified that this result was the same as that analyzed using direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS on two randomly selected DNA samples. The genotype of each sample showed the same result from both methods. Therefore, seven cSNPs were identified from C4B and BAT2 and could be used as the basic data for haplotype analysis of SLA class III region. Moreover, the Multiplex-ARMS method should be powerful for genotyping of genes assigned to the whole SLA region for the xenograft study.

• The Plant Pathology Journal
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• v.28 no.3
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• pp.299-305
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• 2012

Petunia hybrida is commonly used in landscapes and interiors for its attractive flower. Virus-like foliar symptoms, including a mosaic with dark green islands surrounding the veins and chlorosis on the leaf margins, were observed on a petunia plant from Icheon, Gyeonggido, Korea. Cucumber mosaic virus (CMV) was identified in the symptomatic petunia by serological testing for the presence of CMV coat protein (CP) with a direct antibody-sandwich-enzyme-linked immunosorbent assay. An agent was mechanically transmitted to indicator plant species including Chenopodium quinoa. Examination of the inoculated plant leaves by RT-PCR analysis and electron microscopy revealed the presence of specifically amplified CP products and spherical virions of approximately 28 nm in diameter, respectively, providing confirmation of a CMV infection. Analysis of CP sequences showed that CMV petunia isolate (CMVYJC) shared 82.5-100% amino acid sequence identity with CPs of representative CMV strains. Phylogenetic analysis of CPs supports that CMV-YJC is a member of CMV subgroup IA (CMV-IA) and has biological properties of CMV-IA on host species. To our knowledge, this is the first report of CMV from P. hybrida in Korea.

• The Korean Journal of Food And Nutrition
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• v.27 no.2
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• pp.267-273
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• 2014

This study found antibacterial activity of $DMfree^{(R)}$ [green tea extract] on facultative bacteria by direct petri dish method and gene array of obligatory M. leprae infected mesenchymal stem cells (MSC). While DMfree showed DPPH radical scavenging effect and high contents of polyphenol, it did not inhibit growth of facultative bacteria such as E. coli and S. aureus on the petri dish. The result does not exclude a possible antibacterial effect of organic solvent extract of green tea rather than DMfree which comes from the water extract of green tea. Pre-treatment of DMfree appeared to have no effect on copy number of 14 genes compared with control MSC by real-time RT-PCR. However pre-treatment of DMfree on M. leprae infected MSC revealed a significant decrease of anti-inflammatory cytokine (IL-6), (P<0.038) and sharp down-regulation of pro-inflammatory cytokine (IL-1). Enhanced expression of VEGFR-1 mRNA was noted in DMfree pretreated M. leprae infected MSC group (P<0.003). These results show that DMfree would stabilize M. leprae infected MSC from further inflammation by down-regulating anti-inflammatory cytokine (IL-6) and pro-inflammatory cytokine (IL-$1{\beta}$). This is the first report on DMfree inhibition of IL-6 and IL-$1{\beta}$ expression in M. leprae infected MSC. Further experiments that detect protein levels of IL-$1{\beta}$ and IL-6 may support the result of this gene array.

• Imaging Science in Dentistry
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• v.37 no.1
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• pp.35-43
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• 2007

Purpose : To observe direct effect of irradiation on cariogenic Streptooccus mutans. Materials and Methods : S. mutans GS5 was exposed to irradiation with a single absorbed dose of 10, 20, 30, and 40Gy. Viability and changes in antibiotic sensitivity, morphology, transcription of virulence factors, and protein profile of bacterium after irradiation were examined by pour plate, disc diffusion method, transmission electron microscopy, RT-PCR, and SDS-PAGE, respectively. Results : After irradiation with 10 and 20Gy, viability of S. mutans was reduced. Further increase in irradiation dose, however, did not affect the viability of the remaining cells of S. mutans. Irradiated 5. mutans was found to have become sensitive to antibiotics. In particular, the bacterium irradiated with 40Gy increased its susceptibility to cefotaxime, penicillin, and tetracycline. Under the transmission electron microscope, number of morphologically abnormal cells was increased as the irradiation dose was increased. S. mutans irradiated with 10 Gy revealed a change in the cell wall and cell membrane. As irradiation dose was increased, a higher number of cells showed thickened cell wall and cell membrane and Iysis, and appearance of ghost cells was noticeable. In RT-PCR, no difference was detected in expression of gtfB and spap between cells with and without irradiation of 40Gy. In SDS-PAGE, proteins with higher molecular masses were gradually diminished as irradiation dose was increased. Conclusion : These results suggest that irradiation affects the cell Integrity of S. mutans, as observed by SDS-PAGE, and as manifested by the change in cell morphology, antibiotic sensitivity, and eventually viability of the bacterium.

• Imaging Science in Dentistry
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• v.38 no.1
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• pp.39-47
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• 2008

Purpose: The aim of this study was to observe a direct effect of irradiation on the periodontopathic Porphyromonas gingivalis (P. gingivalis). Materials and Methods: P. gingivalis 2561 was exposed to irradiation with a single absorbed dose of 10, 20, 30, and 40Gy. Changes in viability and antibiotic sensitivity, morphology, transcription, and protein profile of the bacterium after irradiation were examined by pour plating method, disc diffusion method, transmission electron microscopy, RT-PCR, and immunoblot, respectively. Results: Viability of irradiated P. gingivalis drastically reduced as irradiation dose was increased. Irradiated P. gingivalis was found to have become more sensitive to antibiotics as radiation dose was increased. With observation under the transmission electron microscope, the number of morphologically abnormal cells was increased with increasing of irradiation dose. In RT-PCR, decrease in the expression of fimA and sod was observed in irradiated P. gingivalis. In immunoblot, change of profile in irradiated P. gingivalis was found in a number of proteins including 43-kDa fimbrillin. Conclusion: These results suggest that irradiation may affect the cell integrity of P. gingivalis, which is manifested by the change in cell morphology and antibiotic sensitivity, affecting viability of the bacterium.

• The Journal of Korean Society of Virology
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• v.29 no.4
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• pp.271-281
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• 1999

The nested polymerase chain reaction (PCR) assay was used to determine the sequences of reverse transcriptase (RT) codons 41, 67, 70, 210, 215 and 219 of human immunodeficiency virus-1 (HIV-1) pol gene. Template DNA was obtained from uncultured peripheral blood mononuclear cells from 27 Korean HIV-1 infected patients treated with ZDV and Korean red ginseng. The second PCRs were done for 2 separated regions (RT codons $13{\sim}98$ and $152{\sim}259$) with $5\;{\mu}l$ of the first PCR productNucleotide sequences were determined by direct sequencing. In the 27 patients, CD4+ cell count decreased from $230{\pm}117/{\mu}l$ to $152{\pm}162/{\mu}l$ for $46{\pm}26$ months (Mo), and actual duration of ZDV intake was $72{\pm}16$ Mo. In the 16 patients who had been treated with ZDV therapy ${\ge}25$ Mo, the incidences of 70R, 215F/Y, and 41L were 61%, 28% and 22%, respectively and those of 67N, 210W and 219Q were 17%. The incidences of 215F/Y were 6.7% for group ${\le}12$ Mo treatment, 22.7% for group with 13 to 24 Mo, and 27.8% for group ${\ge}25$ Mo. There was no mutation in 9 patients. It might be associated with the interruption of ZDV therapy for more than 6 months in 6 patients. This study shows that the detection of mutation could be useful prognostic marker with other clinical and virological data, and very low mutation rate is dectected compared to overseas reports.

• Journal of Life Science
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• v.23 no.4
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• pp.487-494
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• 2013

An AlaAT knock-out mutant (alaat) of rice (Oryza sativa L.) was isolated from T-DNA tagging lines and the genotypes of its progeny were determined with AlaAT1-specific primers. The alaat phenotypes showed decreased growth and grain yield when compared with control plants. The activity of AlaAT1 in the mutant plants was practically undetectable. The responses of alaat plants to growth under salt stress were compared with those of control plants by measuring chlorophyll fluorescence and the activities and mRNA expression of antioxidant enzymes. All abiotic stresses tested (salt, drought, and chilling) caused a similar decrease in chlorophyll fluorescence in both alaat and wild type plants. The activity of peroxidase (POX), an antioxidant enzyme, decreased following salt treatment of alaat plants, while control plant showed an increased activity. The mRNA levels for cAPX (cytosolic ascorbate peroxidase), POX2, and AlaAT were determined by RT-PCR following salt stress. No AlaAT1 mRNA was detected in alaat plants. The POX2 mRNA showed a slightly increased level in the wild type but was not detected in alaat plants, in agreement with the activity assays. The levels of cAPX mRNA were greatly increased in both the wild type and alaat plants. The salt stress effects on rice plant growth are therefore proposed to reflect a loss of function of AlaAT, which alters the activity and synthesis of antioxidant enzymes (especially peroxidases), rather than a direct effect on photosynthesis.

• Research in Plant Disease
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• v.21 no.4
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• pp.315-320
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• 2015

Soybean mosaic virus (SMV) is a prevalent pathogen that causes significant yield reduction in soybean production worldwide. SMV belongs to potyvirus and causes typical symptoms such as mild mosaic, mosaic and necrosis. SMV is seed-borne and also transmitted by aphid. Eleven SMV strains, G1 to G7, G5H, G6H, G7H, and G7a were reported in soybean varieties in Korea. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) method allowed one-step detection of gene amplification by simple procedure and needed only a simple incubator for isothermal template. This RT-LAMP method allowed direct detection of RNA from virus-infected plants without thermal cycling and gel electrophoresis. In this study, we designed RT-LAMP primers named SML-F3/B3/FIP/BIP from coat protein gene sequence of SMV. After the reaction of RT-LAMP, products were identified by electrophoresis and with the detective fluorescent dye, SYBR Green I under daylight and UV light. Optimal reaction condition was at $58^{\circ}C$ for 60 min and the primers of RT-LAMP showed the specificity for nine SMV strains tested in this study.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.6269-6273
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• 2014

Growing evidence suggests that miR-150-5p has an important role in regulating genesis of various types of cancer. However, the roles and the underlying mechanisms of miR-150-5p in development of colorectal cancer (CRC) remain largely unknown. Transwell chambers were used to analyze effects on cell migration and invasion by miR-150-5p. Quantitative real-time PCR (qRT-PCR), Western blotting and dual-luciferase 3' UTR reporter assay were carried out to identify the target genes of miR-150-5p. In our research, miR-150-5p suppressed CRC cell migration and invasion, and MUC4 was identified as a direct target gene. Its effects were partly blocked by re-expression of MUC4. In conclusiomn, miR-150-5p may suppress CRC metastasis through directly targeting MUC4, highlighting its potential as a novel agent for the treatment of CRC metastasis.