• Research in Plant Disease
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• v.26 no.3
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• pp.170-178
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• 2020

Most strawberry viruses exist relatively low titers in tissues, and strawberry tissues include high levels of contamination by polysaccharides and phenolic compounds. These traits make the efficiency of strawberry diagnosis difficult. In this study, we tested different commercially available kits and reagents to secure optimal RNA extraction methods to determine virus detection from strawberry leaves. Total RNA was isolated from leaves of strawberry mottle virus (SMoV)-infected strawberry cultivar 'Mihong'. The efficiency of total RNA for virus diagnosis was confirmed through SMoV detection by one-step or two-step reverse transcription and polymerase chain reaction (RT-PCR). Among those, the RNeasy plant RNA kit was best to isolate RNA and the isolated RNA was good enough for further applications. To ensure a reliable detection for strawberry viruses, synthetic diagnosis clones for major seven strawberry viruses such as strawberry mild yellow edge virus, SMoV, strawberry latent ring spot virus, strawberry crinkle virus, strawberry pallidosis associated virus, strawberry vein banding virus and strawberry necrotic spot virus have been constructed. Based on the synthetic genes in each clone, primer sets for seven strawberry viruses were designed and tested an RT-PCR condition through a simultaneous application of the same annealing temperature that allowed to achieve an efficient and convenient diagnosis.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.56-56
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• 2020

감초는 다년생 콩과(Leguminocae) 식물로 국내에서 시중가격이 높은 만주감초가 일부 재배되고 있다. 우리나라에서 감초 재배법이 불완전한 상황에서 한반도의 기후변화에 의한 온도 상승은 약용작물의 생산 및 품질에 많은 영향을 미칠 것으로 예상되므로 본 연구에서는 재배환경 중 온도 조건만 조절할 수 있는 온도구배터널(temperature gradient tunnel system)을 이용하여 4개의 T1(외기온도+0.5~1.3℃), T2(+1.3~2.2℃), T3(+2.2~3.2℃), T4(+3.2~4.0℃) 처리로 온도구배 하여 4년생 만주감초(Glycyrrhiza uralensis F.)를 재배하였다. 지하부가 오래된 모주와 신초1의 경우 저온(T1)과 중간구간(T2, T3)에서 초장과 총화수가 우세하였고, 번식이 가장 늦은 신초2의 경우 중간구간(T2, T3)에서의 생육 및 개화반응이 뚜렷했다. 각 온도처리구마다 3개의 감초 개체를 선발하여 모주의 정단으로부터 5개의 성엽을 채취하였다. Reverse transcription quantitative PCR (RT-qPCR)은 AccuPower® GreenStar^TM RT-qPCR Master Mix (Bioneer, Korea)를 이용하여 진행되었다. Primer 디자인은 NCBI Primer-blast 프로그램을 사용해 제작하였고 ABI StepOne real time system (Applied Biosystem)의 melting curve analysis에서 one-peak test를 통해 gene specific primer임을 확인하였다. 각 온도처리구의 감초 잎에서 RNA를 추출하였고, RT-qPCR을 통해 감초의 유전자 발현양상을 비교, 분석하였다. Phytochrome interacting factor 4 (PIF4)는 식물 호르몬을 유발하는 전사조절을 조정함으로써 고온 신호전달에 핵심적인 역할을 수행한다. 활성화된 Phytochrome B(PhyB)는 PIF4의 활성을 억제한다고 알려졌다. Eukaryotic initiation factors(eIFs)는 mRNA 번역 개시인자로 유전자 발현과 특정 단백질 생산을 조절하는 역할을 한다. 본 결과는 온도조건에서 반응하는 생리적 변화를 전사체 수준에서 조사 분석하여 생리해석의 기초자료로 활용, 국내 감초 재배를 위한 환경조건 구명 및 적지 선정 기초자료로서 활용을 기대한다.

• Journal of Microbiology and Biotechnology
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• v.20 no.10
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• pp.1450-1456
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• 2010

Accurate and rapid diagnosis of Pandemic Influenza A/H1N1 2009 virus (H1N1 2009) infection is important for the prevention and control of influenza epidemics and the timely initiation of antiviral treatment. This study was conducted to evaluate the performance of several diagnostic tools for the detection of H1N1 2009. Flocked nasopharyngeal swabs were collected from 254 outpatients of suspected H1N1 2009 during October 2009. This study analyzed the performances of the RealTime Ready Inf A/H1N1 Detection Set (Roche), Influenza A (H1N1) Real-Time Detection Kit (Bionote), Seeplex Influenza A/B OneStep Typing Set [Seeplex Reverse Transcriptase PCR (RT-PCR)], BinaxNow Influenza A & B Test Kit [Binax Rapid Antigen Test (RAT)], and SD BIOLINE Influenza Ag kit (SD RAT). Roche and Bionote real-time RT-PCR showed identical results for the H1N1 2009 hemagglutinin gene. Compared with real-time RT-PCR, the sensitivities and specificities were 83.7% and 100% for Seeplex RT-PCR, 64.5% and 94.7% for Binax RAT, and 69.5% and 100% for SD RAT. The sensitivities of Seeplex RT-PCR, Binax RAT, and SD RAT in patients aged over 21 years were 73.7%, 47.4%, and 57.9%, respectively. The sensitivities of Seeplex RT-PCR, Binax RAT, and SD RAT on the day of initial symptoms were mostly lower (68.8%, 56.3%, and 31.3%, respectively). In conclusion, multiplex RT-PCR and RAT for the detection of H1N1 2009 were significantly less sensitive than real-time RT-PCR. Moreover, a negative RAT may require more sensitive confirmatory assays, because it cannot be ruled out from influenza infection.

• Korean Journal of Food Science and Technology
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• v.37 no.6
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• pp.1018-1023
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• 2005

Simplified procedure was developed for concentrating and detecting poliovirus and norovirus in oysters. Viruses were seeded into oyster tissue homogenates and concentrated through polyethylene glycol (PEG) precipitation, chloroform or Freon extraction, with additional PEG precipitation. Amount of viruses was evaluated using poliovirus plaque assay. Virus recovery during concentration procedure was approximately 16.4-26.0%. For defection, viral RNAs in oysters were examined using one-step RT-PCR after extraction with Trizol. Dilution or capturing of viral RNA using silica gel membrane allowed viruses to be detected by RT-PCR, whereas viruses could not be removed using $QIAshredder^{TM}$ Homogenizer, which is effective in removing RT-PCR inhibitors in lettuce and hamburgers. Freon extraction, generally used to concentrate viruses found in food, could be substituted with chloroform extraction using this procedure; no difference could be observed between detection limits of whole oyster extracts and digestive organ extracts indicating that RT-PCR inhibitors were distributed evenly throughout whole tissues. Nested PCR greatly improved efficiency of this procedure. Overall, this procedure could remove sufficient amount of inhibitors to allow detection of norovirus in oysters.

• Journal of Veterinary Science
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• v.21 no.2
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• pp.22.1-22.9
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• 2020

Rabid raccoon dogs (Nyctereutes procyonoides koreensis) have been responsible for animal rabies in South Korea since the 1990s. A recombinant rabies vaccine strain, designated as ERAGS, was constructed for use as a bait vaccine. Therefore, new means of differentiating ERAGS from other rabies virus (RABV) strains will be required in biological manufacturing and diagnostic service centers. In this study, we designed two specific primer sets for differentiation between ERAGS and other RABVs based on mutation in the RABV glycoprotein gene. Polymerase chain reaction analysis of the glycoprotein gene revealed two DNA bands of 383 bp and 583 bp in the ERAGS strain but a single DNA band of 383 bp in the field strains. The detection limits of multiplex reverse transcription polymerase chain reaction (RT-PCR) were 80 and 8 FAID₅₀/reaction for the ERAGS and Evelyn-Rokitnicki-Abelseth strains, respectively. No cross-reactions were detected in the non-RABV reference viruses, including canine distemper virus, parvovirus, canine adenovirus type 1 and 2, and parainfluenza virus. The results of multiplex RT-PCR were 100% consistent with those of the fluorescent antibody test. Therefore, one-step multiplex RT-PCR is likely useful for differentiation between RABVs with and those without mutation at position 333 of the RABV glycoprotein gene.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.595-602
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• 2005

A one-step real-time quantitative RT-PCR assay in combination with automated RNA extraction was evaluated for routine testing of HCV RNA in the laboratory. Specific primers and probes were developed to detect 302 bp on 5'-UTR of HCV RNA. The assay was able to quantitate a dynamic linear range of $10^7-10^1$ HCV RNA copies/reaction ($R^2=0.997$). The synthetic HCV RNA standard of $1.84{\pm}0.1\;(mean{\pm}SD)$ copies developed in this study corresponded to 1 international unit (IU) of WHO International Standard for HCV RNA (96/790 I). The detection limit of the assay was 3 RNA copies/reaction (81 IU/ml) in plasma samples. The assay was comparable to the Amplicor HCV Monitor (Monitor) assay with correlation coefficient r=0.985, but was more sensitive than the Monitor assay. The assay could be completed within 3 h from RNA extraction to detection and data analysis for up to 32 samples. It allowed rapid RNA extraction, detection, and quantitation of HCV RNA in plasma samples. The method provided sufficient sensitivity and reproducibility and proved to be fast and labor-saving, so that it was suitable for high throughput HCV RNA test.

• Clinical and Experimental Reproductive Medicine
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• v.29 no.4
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• pp.295-302
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• 2002

Uterine cells carry out proliferation and differentiation for preparation the embryonic implantation during pregnancy. Therefore regulation of the cell proliferation is an essential step for uterine preparation, but there is not much information about the proliferation related genes in pregnant uterus. To identify these implantation specific genes, a PCR-select cDNA subtraction method was employed and got a few genes. One of the identified genes is a novel gene encoding oral tumor suppressor doc-1. To detect the doc-1 expression on the pregnant uterus, dot blotting, RT-PCR, and in situ hybridization were employed. Dot blotting revealed that doc-1 mRNA expression increase after implantation. During normal pregnancy, doc-1 mRNA expression was detected as early as day 1 of pregnancy with RT-PCR. Its expression was increased about 15 times after embryonic implantation. doc-1 transcript was localized in luminal epithelial cells but it was very faint during preimplantation. After starting the implantation, it localized in the stromal cells; heightened expression of doc-1 correlates with intense stromal cell proliferation surrounding the implanting blastocyst on day 6 morning. However in the decidualized cells, the intensity of localized doc-1 mRNA was weak. From those results, it is revealed that doc-1 express at pregnant uterus of the mouse. In addition it is suggested that doc-1 is the gene regulating the proliferation of the luminal epithelial cells and stromal cells during early implantation and decidualization.

• Journal of fish pathology
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• v.34 no.2
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• pp.133-140
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• 2021

With the recent isolation of a new betanodavirus in shellfish, Korean Shellfish Nervous Necrosis Virus (KSNNV), it has also been identified the reassortant KSNNV of two RNA segments, in which one segment is KSNNV genotype but the other one is known genotype. In this study, we confirmed that the ressortant KSNNVs obtained in previous screening study of our laboratory for betanodaviruses in shellfish were KS/RGNNV and RG/KSNNV type by performing two consecutive multiplex RT-PCR on each RNA1 and RNA2 segment (R1- and R2-discriminative multiplex two-step RT-PCR, respectively) to determine the genotype of each segment based on the size of amplicon. In the pathogenicity analysis, none of the reassortants induced specific external symptoms or mortality of VNN, but viruses of 2 × 10⁴~10⁵ copies/mg or more were detected at 14 days after injection (10⁷ copies/fish) in brain tissues of 4 species except for crucian carp and common carp among the 6 species of juvenile fish used. In addition, the histopathological features of weak but distinct vacuole formation were also found in the brain of these infected fish, but no difference was found between the two reassortants KS/RGNNV-KG and RG/KSNNV-CM.

• Journal of Food Hygiene and Safety
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• v.30 no.2
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• pp.150-158
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• 2015

This article reports the development of an effective test procedure for detection of norovirus (NoV) in foods of diverse matrices. In this study, target foods included fermented milk, soybean paste, powders made from uncooked grains and vegetables, sesame leaves preserved in soy sauce, pickled mooli, and mooli. Viral recovery varied depending on the food matrices or elution buffers tested. Buffers were compared to determine effective elution buffers from artificially virus-contaminated foods. The conventional test procedure for concentrating viruses from food (elution-polyethylene glycol(PEG) precipitation-chloroform-PEG precipitation) was modified to save time by eliminating one PEG precipitation step. The modified procedure (elution-chloroform-PEG precipitation) was able to concentrate viruses more effectively than the conventional procedure. It also removed RT-PCR inhibitors effectively. The modified procedure was applied to target food for genogroup II NoV detection. NoV RNA was detected at the initial inoculum levels 3.125-12.5 RT-PCR units per 10-25 g tested food. The use of this newly established procedure should facilitate detection of low levels of norovirus in diverse foods.

• Journal of fish pathology
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• v.31 no.1
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• pp.9-13
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• 2018

We previously monitored nervous necrosis virus (NNV) in brain samples of artificially produced walleye Pollock (Gadus chalcogrammus) seedlings, with a low prevalence (1.8%, 1/55) but no clinical symptoms. Given that this virus is considered one of the most serious viral threats for almost all marine aquaculture fish species and characterized by both vertical and horizontal transmission, it would be interesting to monitor NNV in the fertilized eggs as well. We collected fertilized walleye pollock eggs from the farms located in Goseong during January to March, 2017. Approximately 50 mg of eggs were periodically taken from 4 each different batches, and 37 different pooled sample sets in total were made during sampling period. RNA was extracted from the eggs by using Trizol and cDNA was synthesized for RT-PCR for detecting NNV. Primers and PCR conditions are the same as previously described. As a result, NNV was not detected from any of the sample sets by one step PCR (0%, 0/37), suggesting NNV may not be a threat in walleye pollock aquaculture in Korea at present time. However, continuous monitoring for NNV should be conducted because introducing a new species into aquaculture industry involves potentials of disease outbreak and NNV is already known to cause outbreaks in gadoid fishes.