• The Plant Pathology Journal
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• v.35 no.2
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• pp.164-171
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• 2019

An assay for detecting Apple scar skin viroid (ASSVd) was developed based on nucleic acid sequence based amplification (NASBA) in combination with realtime detection during the amplification process using molecular beacon. The ASSVd specific primers for amplification of the viroid RNA and molecular beacon for detecting the viroid were designed based on highly conserved regions of several ASSVd sequences including Korean isolate. The assay had a detection range of $1{\times}10^4$ to $1{\times}10^{12}$ ASSVd RNA $copies/{\mu}l$ with reproducibility and precision. Following the construction of standard curves based on time to positive (TTP) value for the serial dilutions ranging from $1{\times}10^7$ to $1{\times}10^{12}$ copies of the recombinant plasmid, a standard regression line was constructed by plotting the TTP values versus the logarithm of the starting ASSVd RNA copy number of 10-fold dilutions each. Compared to the established RT-PCR methods, our method was more sensitive for detecting ASSVd. The real-time quantitative NASBA method will be fast, sensitive, and reliable for routine diagnosis and selection of viroid-free stock materials. Furthermore, real-time quantitative NASBA may be especially useful for detecting low levels in apple trees with early viroid-infection stage and for monitoring the influence on tree growth.

• The Plant Pathology Journal
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• v.40 no.1
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• pp.40-47
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• 2024

Garlic can be infected by a variety of viruses, but mixed infections with leek yellow stripe virus, onion yellow dwarf virus, and allexiviruses are the most damaging, so an easy, inexpensive on-site method to simultaneously detect at least these three viruses with a certain degree of accuracy is needed to produce virus-free plants. The most common laboratory method for diagnosis is multiplex reverse transcription polymerase chain reaction (RT-PCR). However, allexiviruses are highly diverse even within the same species, making it difficult to design universal PCR primers for all garlic-growing regions in the world. To solve this problem, we developed an inexpensive on-site detection system for the three garlic viruses that uses a commercial mobile PCR device and a compact electrophoresis system with a blue light. In this system, virus-specific bands generated by electrophoresis can be identified by eye in real time because the PCR products are labeled with a fluorescent dye, FITC. Because the electrophoresis step might eventually be replaced with a lateral flow assay (LFA), we also demonstrated that a uniplex LFA can be used for virus detection; however, multiplexing and a significant cost reduction are needed before it can be used for on-site detection.

• Journal of Plant Biotechnology
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• v.33 no.1
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• pp.57-62
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• 2006

Several methods for determining the response of corn to glyphosate were investigated to provide a fast and reliable method for identifying glyphosate-resistant corn in vivo. Two bioassays were developed. One assay is named 'whole plant / leaf growth assay', in which the herbicide glyphosate is applied on the upper part of 3rd leaf and the growth of herbicide-untreated 4th leaf is measured at 3 day after treatment. in this assay, the leaf growth of conventional corn was inhibited in a dose dependent from 50 to $1600{\mu}g/mL$ of glyphosate and growth inhibition at $1600{\mu}g/mL$ was 55% of untreated control. The assay has the potential to be used especially in the case that the primary cause of glyphosate resistance is related with a reduction of the herbicide translocation. Another assay is named 'leaf segment / shikimate accumulation assay', in which the four excised leaf segments ($4{\times}4mm$) are placed in each well of a 48-well microtiter plate containing $200{\mu}L$ test solution and the amount of shikimate is determined after incubation for 24 h in continuous light at $25^{\circ}C$. In this assay, 0.33% sucrose added to basic test solution enhanced a shikimate accumulation by 3 to 4 times and the shikimate accumulation was linearly occurred from 2 to $8{\mu}g/mL$ of glyphosate, showing an improved response to the method described by Shaner et al. (2005). The leaf segment / shikimate accumulation assay is simple and robust and has the potential to be used as a high throughput assay in the case that the primary cause of glyphosate resistance is related with EPSPS, target site of the herbicide. Taken together, these two assays would be highly useful to initially select the lines obtained after transformation, to investigate the migration of glyphosate-resistant gene into other weeds and to detect a weedy glyphosate-resistant corn in field.

• Toxicological Research
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• v.21 no.2
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• pp.99-105
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• 2005

Photo-mutagenic compounds have been known to alter skin cancer rates by acting as initiators or by affecting subsequent steps in carcinogenesis. The objectives of this study are to investigate the utility of photo-chromosomal aberration (photo-CA) assay for detecting photo-clastogens, and to evaluate its ability to predict rodent photocarcinogenicity. Photo-CA assay was performed with five test substances that demonstrated positive results in photo-carcinogenicity tests: 8-Methoxypsoralen (photoactive substance that forms DNA adducts in the presence of ultraviolet A irradiation), chlorpromazine (an aliphatic phenothiazine an alpha-adrenergic blocking agent), lomefloxacin (an antibiotic in a class of drugs called fluoroquinolones), anthracene (a tricyclic aromatic hydrocarbon a basic substance for production of anthraquinone, dyes, pigments, insecticides, wood preservatives and coating materials) and Retinoic acid (a retinoid compound closely related to vitamin A). For the best discrimination between the test substance-mediated genotoxicity and the undesirable genotoxicity caused by direct DNA absorption, a UV dose-response of the cells in the absence of the test substances was firstly analyzed. All 5 test substances showed a positive outcome in photo-CA assay, indicating that the photo-CA test is very sensitive to the photo-genotoxic effect of UV irradiation. With this limited data-set, an investigation into the predictive value of this photo-CA test for determining the photo-carcinogenicity showed that photo-CA assay has the high ability of a test to predict carcinogenicity. Therefore, the photo-CA test using mammalian cells seems to be a sensitive method to evaluate the photo-carcinogenic potential of new compounds.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.816-824
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• 2017

Human noroviruses are widespread and contagious viruses causing nonbacterial gastroenteritis. Real-time reverse transcription quantitative PCR (real-time RT-qPCR) is currently the gold standard for the sensitive and accurate detection of these pathogens and serves as a critical tool in outbreak prevention and control. Different surveillance teams, however, may use different assays, and variability in specimen conditions may lead to disagreement in results. Furthermore, the norovirus genome is highly variable and continuously evolving. These issues necessitate the re-examination of the real-time RT-qPCR's robustness in the context of accurate detection as well as the investigation of practical strategies to enhance assay performance. Four widely referenced real-time RT-qPCR assays (Assays A-D) were simultaneously performed to evaluate characteristics such as PCR efficiency, detection limit, and sensitivity and specificity with RT-PCR, and to assess the most accurate method for detecting norovirus genogroups I and II. Overall, Assay D was evaluated to be the most precise and accurate assay in this study. A ZEN internal quencher, which decreases nonspecific fluorescence during the PCR, was added to Assay D's probe, which further improved the assay performance. This study compared several detection assays for noroviruses, and an improvement strategy based on such comparisons provided useful characterizations of a highly optimized real-time RT-qPCR assay for norovirus detection.

• Applied Biological Chemistry
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• v.46 no.2
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• pp.74-78
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• 2003

To determine the urease inhibitory activity of various heavy metal ions, a photometric cuvette assay for measuring ammonia production was developed. In this assay, the absorbance values at 630 m were linearly increased according to the ammonia concentrations up to 3.0 mg/l (r : 0.998). The urease inhibitions upon addition of a single species of heavy metal ions were in the decreasing order of Hg(II) > Pb(II) > Cu(II) > Cd(II) > Zn(II) ions. As expected, the urease inhibitions at a fixed concentration of a single species and at varying concentrations of other species occurred in the additive way. The above results show the applicability of the current method to the selective detection on Hg(II) ions as well as the screening of heavy metal ions possibly present at various samples.

• Journal of Korean Biological Nursing Science
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• v.3 no.2
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• pp.21-33
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• 2001

The objective of this study was to examine the effects of antioxidant vitamins on the cellular oxidant damage by observing the mitogenicity in the mouse spleen and the strand breaks of DNA in mouse blood induced by $AFB_2$. Intraperitoneal(i.p.) injections of vitamin C(VC) of 10 mg/kg and vitamin E(VE) of 63.8 mg/kg were repeatedly administered to male ICR mice of 6 weeks old at intervals of 4 times every 2 days. After one hour vitamin treatments, $AFB_1$ of 0.4 mg/kg was injected into the $AFB_2$ plus vitamin treated groups in the same way. On the other hands, into the $AFB_2$ only treated group, only $AFB_2$ was injected without vitamins in the same method as above. The results of the experiment are as follows ; as regard to comet assay, DNA strand breaks were clearly present and they formatted a typical comet tail in the mice blood of the $AFB_2$ only treated groups. However, comet tails apparently disappeared in $AFB_2$ plus antioxidant vitamins treated groups since oxidant damage was controlled in an almost similar level to the control group. Mitogenicity of the spleen also showed a similar tendency as before, and these differences were more remarkably observed in the reaction against Con-A, which is a T-cell mitogen. In these data, the statistical significance was p<0.01. The LDL and VLDL levels were 408.72, 504.47 mg/dl respectively in the $AFB_2$ only treated groups. Compared with the $AFB_1$ only treated groups, those of $AFB_2$ plus antioxidant vitamin treated groups decreased to 272.06(VC), 305.28 mg/dl(VE), respectively. On the other hand, HDL levels were diminished to 32.60, 29.60 mg/dl in $AFB_2$ only treated groups, compared to 42.23, 41.14 mg/dl in the $AFB_2$ plus antioxidant vitamins treated groups. But, blood glucose levels were not statistically significant.

• Toxicological Research
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• v.20 no.3
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• pp.225-232
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• 2004

The suitability of the single cell gel electrophoresis (SCGE) assay as a test for the monitoring of genotoxicity of aquatic environment was evaluated. The SCGE assay was employed to detect DNA damage induced in clam (Spisula sachalinensis) exposed to a direct mutagen, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) or an indirect mutagen, benzo[a]pyrene (B[a]P). The cells of gill and digestive glands were isolated from clam by homogenization, which was the optimized cell dissociation method, and the level of DNA damage was assessed and expressed as mean tail length. In the gill cells, significant dose- and time-dependent increase was observed in the mean tail length at the concentration from 0.01 to 0.5 ppm MNNG for 96 h. The linear correlation between relative dam-age index (RDI) values was suggested to provide criteria of genotoxicity monitoring for direct acting mutagen. The dose- and time-dependent responses of the digestive glands cells were less sensitive than those of the gill cells. In contrast, the genotoxic response resulting from the exposure of 0.01～1.0 ppm B[a]P to clam revealed a higher sensitivity in the digestive glands cells than the gill cells. The comparison between the time profiles of genotoxic responses in clam and carp, the latter had been obtained in our previous study, indicated that the metabolism of genotoxic compounds in the two aquatic organisms were quite different each other. We conclude that the SCGE assay has the potential as a screening test for routine genotoxicity monitoring of aquatic organisms because of its higher sensitivity and simplicity.

• Food Science of Animal Resources
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• v.30 no.4
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• pp.590-596
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• 2010

Meat and meat products are a potential source of food-borne pathogens, including Staphylococcus aureus, Salmonella spp., Escherichia coli O157:H7, and Bacillus cereus. A sensitive and specific PCR assay for the detection of these pathogens in meat and meat products was developed in this study, as part of a broader effort to reduce the potential health hazards posed by these pathogens. Initially, PCR conditions were standardized with purified DNA. Under standard conditions, the detection level for PCR was as low as 10 pg of purified bacterial DNA. After overnight growth of bacteria in a broth medium, as few as $10^2$ CFU of bacteria were detected by PCR assay. The primers employed in the PCR assay were found to be highly specific for individual organisms, and evidenced no cross-reactivity with heterologous organisms. Additionally, the multiplex PCR assays also amplified some target genes from the four pathogens, and multiplex amplification was obtained from as little as 10 pg of DNA, thus illustrating the excellent specificity and high sensitivity of the assay. In conclusion, this PCR-based technique provides a sensitive and specific method for the detection of S. aureus, Salmonella spp., E. coli O157:H7, and B. cereus in meat and meat products.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1411-1416
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• 2014

Gender selection is important in livestock industries; for example, female calves are required in the dairy industry. Sex-sorted semen is commonly used for the production of calves of the desired gender. However, assessment of the sex ratio of the sorted semen is tedious and expensive. In this study, a rapid, cost effective and reliable method for determining the sex ratio was developed using a multiplex real-time polymerase chain reaction (PCR) assay. In this assay, the X and Y chromosome-specific markers, i.e., bovine proteolipid protein (PLP) gene and sex-determining region Y (SRY) were simultaneously quantified in a single tube. The multiplex real-time PCR assay was shown to have high amplification efficiencies (97% to 99%) comparable to the separated-tube simplex real-time PCR assay. The results obtained from both assays were not significantly different (p>0.05). The multiplex assay was validated using reference DNA of known X ratio (10%, 50%, and 90%) as templates. The measured %X in semen samples were the same within 95% confidence intervals as the expected values, i.e., >90% in X-sorted semen, <10% in Y-sorted semen and close to 50% in the unsorted semen. The multiplex real-time PCR assay as shown in this study can thus be used to assess purity of sex-sorted semen.