• Mycobiology
• /
• v.41 no.2
• /
• pp.86-93
• /
• 2013

Sequence characterized amplified region (SCAR) markers are one of the most effective and accurate tools for microbial identification. In this study, we applied SCAR markers for the rapid and accurate detection of Phytophthora katsurae, the casual agent of chestnut ink disease in Korea. In this study, we developed seven SCAR markers specific to P. katsurae using random amplified polymorphic DNA (RAPD), and assessed the potential of the SCAR markers to serve as tools for identifying P. katsurae. Seven primer pairs (SOPC 1F/SOPC 1R, SOPC 1-1F/SOPC 1-1R, SOPC 3F/SOPC 3R, SOPC 4F/SOPC 4R, SOPC 4F/SOPC 4-1R, SOPD 9F/SOPD 9R, and SOPD 10F/SOPD 10R) from a sequence derived from RAPD fragments were designed for the analysis of the SCAR markers. To evaluate the specificity and sensitivity of the SCAR markers, the genomic DNA of P. katsurae was serially diluted 10-fold to final concentrations from 1 mg/mL to 1 pg/mL. The limit of detection using the SCAR markers ranged from $100{\mu}g/mL$ to 100 ng/mL. To identify the limit for detecting P. katsurae zoospores, each suspension of zoospores was serially diluted 10-fold to final concentrations from $10{\times}10^5$ to $10{\times}10^1$ zoospores/mL, and then extracted. The limit of detection by SCAR markers was approximately $10{\times}10^1$ zoospores/mL. PCR detection with SCAR markers was specific for P. katsurae, and did not produce any P. katsurae-specific PCR amplicons from 16 other Phytophthora species used as controls. This study shows that SCAR markers are a useful tool for the rapid and effective detection of P. katsurae.

• Applied Biological Chemistry
• /
• v.49 no.3
• /
• pp.192-195
• /
• 2006

For the development of a qualitative PCR detection method for genetically modified perilla (Perilla frutescens), perilla species-specific gene, KAS-I (Beta-ketoacyl-ACP synthase I), was selected and validated as suitable for the use as an endogenous reference gene in perilla. Primer specificity was first tested by the means of qualitative PCR analysis. The primer pair Pfru3-F/R amplifying the perilla endogenous gene, KAS-I, gave rise to an amplicon 95 bp. No amplified product was observed when DNA samples from 15 different plants were used as templates. Qualitative PCR detection method was assayed with vitamin E-enriched GM Perilla developed in Korea. For the qualitative PCR detection method, the construct-specific detection primer pairs were constructed. The primer pair TMTO-F/R amplifying the junction region of TMT (${\gamma}$-tocopherol methyltransferase) gene and OCS (Octopine synthase) terminator introduced in GM perilla gave rise to an amplicon 148 bp.

• Proceedings of the KSRS Conference
• /
• 2003.11a
• /
• pp.654-655
• /
• 2003

Korea has experienced 10 a Cochlodinium polykrikoides red tide outbreaks during the last 10 years (1993-2002). The monitoring activities at National Fisheries Research and Development Institute (NFRDI) in Korea have been extended to all the coastal waters after the worst of fish killing by C. polykrikoides blooms in 1995. NFRDI is looking forward to finding out the feasibility of red tide detection around Korean waters using satellite remote sensing of NOAA/AVHRR, Orbview-2/SeaWiFS, IRS-P4/OCM and Terra/MODIS on real time base. In this study, we used several alternative methods including climatological analysis, spectral and optical methods which may offer a potential detection of the major species of red tide in Korean waters. The relationship between the distribution of SST and C. polykrikoides bloom areas was studied. In climatological analysis, NOAA, SeaWiFS, OCM satellite data in 20th and 26th August 2001 were chosen using the known C. polykrikoides red tide bloom area mapped by helicopter reconnaissance and ground observation. The 26th August, 2001 SeaWiFS chlorophyll a anomaly imageries against the imageries of non-occurring red tide for August 20, 2001 showed the areas C. polykrikoides occurred. The anomalies of chlorophyll a concentration from satellite data between before and after red tide outbreaks showed the similar distribution of C. polykrikoides red tide in 26th August, 2001. The distribution of the difference in SST between daytime and nighttime also showed the possibility of red tide detection. We used corrected vegetation index (CVI) to detect floating vegetation and submerged vegetation containing algal blooms. The simple result of optical absorption from C. polykrikoides showed that if we use the optical characteristics of each red tide we will be able to get the feasibility of the red tide detection.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.12
• /
• pp.1672-1683
• /
• 2021

Vibrio parahaemolyticus is recognized as one of the most important foodborne pathogens responsible for gastroenteritis in humans. The bla_CARB-17 gene is an intrinsic β-lactamase gene and a novel species-specific genetic marker of V. parahaemolyticus. In this study, a loop-mediated isothermal amplification (LAMP) assay combined with a lateral flow dipstick (LFD) was developed targeting this bla_CARB-17 gene. The specificity of LAMP-LFD was ascertained by detecting V. parahaemolyticus ATCC 17802 and seven other non-V. parahaemolyticus strains. Finally, the practicability of LAMP-LFD was confirmed by detection with V. parahaemolyticus-contaminated samples and natural food samples. The results showed that the optimized reaction parameters of LAMP are as follows: 2.4 mmol/l Mg²⁺, 0.96 mmol/l dNTPs, 4.8 U Bst DNA polymerase, and an 8:1 ratio of inner primer to outer primer, at 63℃ for 40 min. The optimized reaction time of the LFD assay is 60 min. Cross-reactivity analysis with the seven non-V. parahaemolyticus strains showed that LAMP-LFD was exclusively specific for V. parahaemolyticus. The detection limit of LAMP-LFD for V. parahaemolyticus genomic DNA was 2.1 × 10^-4 ng/μl, corresponding to 630 fg/reaction and displaying a sensitivity that is 100-fold higher than that of conventional PCR. LAMP-LFD in a spiking study revealed a detection limit of approximately 6 CFU/ml, which was similar with conventional PCR. The developed LAMP-LFD specifically identified the 10 V. parahaemolyticus isolates from 30 seafood samples, suggesting that this LAMP-LFD may be a suitable diagnostic method for detecting V. parahaemolyticus in aquatic foods.

• Proceedings of the KSAR Conference
• /
• 2002.06a
• /
• pp.197.2-198
• /
• 2002

• 한국생물공학회:학술대회논문집
• /
• 2000.11a
• /
• pp.711-712
• /
• 2000

DNA probe assay comprising a microwell as' solid matrix for the immobilization of streptavidin (SA) and an oligonucleotide with covalently bound fluorecein as detection probe was developed. The insolubilized SA captured the biotinylated DNA product of polymerase chain reaction (PCR), and the product was denatured under a basic condition. The remaining single-stranded DNA on the solid surface was hybridized with the probe for signal generation that was performed based on enzyme-linked immuno -reactions.

• Journal of Forest and Environmental Science
• /
• v.31 no.1
• /
• pp.68-71
• /
• 2015

Korean L. leiolepis of the genus Leontopodium could be discriminate from the foreign L. alpinum using random amplified polymorphic DNA (RAPD). Among the 12 URP markers used for the detection, the URP-5 marker and the URP-7 marker detected polymorphic DNA bands, ranging from 400-1000 bp in the size of amplified DNA fragments.

• 축산식품과학과 산업
• /
• v.4 no.2
• /
• pp.56-64
• /
• 2015

• Proceedings of the Zoological Society Korea Conference
• /
• 1999.10b
• /
• pp.101.1-101
• /
• 1999

No Abstract, See Full Text

• Bulletin of the Korean Chemical Society
• /
• v.10 no.2
• /
• pp.196-200
• /
• 1989

Some s-triazine herbicides, namely simazine, atrazine, and propazine present as trace components in a complex mixture were analyzed by GC/MS and GC/MS/MS methods. Even though monitoring the molecular ions was the best in terms of sensitivity, adequate analysis could not be done when interfering species were present. When doubly charged ions which appeared at characteristic m/z values were monitored, chromatograms were rather free from interference. More importantly, selected reaction monitoring was found to provide a selective means of detection with general applicability.