• The Plant Pathology Journal
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• v.33 no.3
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• pp.307-317
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• 2017

Satsuma dwarf virus (SDV) or Citrus mosaic sadwavirus (CiMV) were not consistently detected in RTPCR assay with the primer sets based on gene of Japan isolates. SDV and CiMV isolates were distinctively divided into two groups based on phylogenetic analysis of PP2 gene cloned from 22 Korean isolates, and the Korean CiMV and SDV isolates shared 95.5-96.2% and 97.1-97.7% sequence identity with Japanese isolate, respectively. We developed PP2-1 primer set based on the PP2 gene sequence of Korean isolates to simultaneously and effectively detect SDV and CiMV. And CTLV-2013 and CTV-po primer sets were newly designed for detection of Citrus tatter leaf virus (CTLV) and Citrus tristeza virus (CTV), respectively. Using these primer sets, a new multiplex PCR assay was developed as a means to simultaneously detect 4 citrus viruses, CTV, CTLV, SDV, and CiMV. The degree of detection by the multiplex PCR were consistent with those of uniplex RT-PCR for detection of each of the viruses. Therefore, the new multiplex PCR provides an efficient method for detecting 4 citrus viruses, which will help diagnose many citrus plants at the same time. We verified that 35.2% and 72.1% of 775 trees in 155 orchards were infected with SDV or CiMV (SDV/CiMV) and CTV by the multiplex-PCR assay, respectively, and CTLV was not detected in any of the trees tested.

• Korean Journal of Food Science and Technology
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• v.31 no.6
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• pp.1628-1634
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• 1999

The polymerase chain reaction (PCR) for the sensitive and specific detection of Listeria monocytogenes was employed by using LM 1 and LM 2 primers which were based on the listeriolysin O gene. The direct use of cell suspension as DNA template, without DNA extraction or lysis step, was suitable and specific enough to detect L. monocytogenes at the level of $10^2$ CFU or less per PCR for the pure culture and milk sample, however, the detection sensitivity became blunt for other food samples such as kimchi and chicken. The nested PCR, in which L-1 and L-2 (both designed from listeriolysin O gene) were employed as inner primers, was specific for detecting L. monocytogenes and enhanced the detection limit by 10 times. The PCR using LM 1 and LM 2 primers was very effective to detect L. monocytogenes from foods in terms of the specificity and time consumed, i. e. within $4{\sim}8\;hrs$ (nested PCR).

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.6
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• pp.891-895
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• 2019

Objective: Aim of present study was the set up of a fast and reliable protocol using species-specific markers for the quali-quantitative analysis of DNA and the detection of ruminant biological components in dairy products. For this purpose, the promoter of the gene coding for the ${\alpha}$-lactoalbumin (LALBA) was chosen as possible candidate for the presence of short interspersed nuclear elements (SINEs). Methods: DNA was isolated from somatic cells of 120 individual milk samples of cattle (30), Mediterranean river buffalo (30), goat (30), and sheep (30) and the gene promoter region (about 600/700 bp) of LALBA (from about 600 bp upstream of exon 1) has been sequenced. For the development of a single polymerase chain reaction (PCR) protocol that allows the simultaneous identification of DNA from the four species of ruminants, the following internal primers pair were used: 5'-CACTGATCTTAAAGCTCAGGTT-3' (forward) and 5'-TCAGA GTAGGCCACAGAAG-3' (reverse). Results: Sequencing results of LALBA gene promoter region confirmed the presence of SINEs as monomorphic "within" and variable in size "among" the selected species. Amplicon lengths were 582 bp in cattle, 592 bp in buffalo, 655 in goat and 729 bp in sheep. PCR specificity was demonstrated by the detection of trace amounts of species-specific DNA from mixed sources ($0.25ng/{\mu}L$). Conclusion: We developed a rapid PCR protocol for the quali-quantitative analysis of DNA and the traceability of dairy products using a species-specific marker with only one pair of primers. Our results validate the proposed technique as a suitable tool for a simple and inexpensive (economic) detection of animal origin components in foodstuffs.

• Journal of Microbiology and Biotechnology
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• v.22 no.8
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• pp.1113-1117
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• 2012

Shigella sonnei is a causal agent of fever, nausea, stomach cramps, vomiting, and diarrheal disease. The present study describes a quantitative polymerase chain reaction (qPCR) assay for the specific detection of S. sonnei using a primer pair based on the methylase gene for the amplification of a 325 bp DNA fragment. The qPCR primer set for the accurate diagnosis of Shigella sonnei was developed from publically available genome sequences. This quantitative PCR-based method will potentially simplify and facilitate the diagnosis of this pathogen and guide disease management.

• Mycobiology
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• v.50 no.5
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• pp.382-388
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• 2022

White mold (or Sclerotinia stem rot), caused by Sclerotinia species, is a major air, soil, or seed-transmitted disease affecting numerous crops and wild plants. Microscopic or culture-based methods currently available for their detection and identification are time-consuming, laborious, and often erroneous. Therefore, we developed a multiplex quantitative PCR (qPCR) assay for the discrimination, detection, and quantification of DNA collected from each of the three economically relevant Sclerotinia species, namely, S. sclerotiorum, S. minor, and S. nivalis. TaqMan primer/probe combinations specific for each Sclerotinia species were designed based on the gene sequences encoding aspartyl protease. High specificity and sensitivity of each probe were confirmed for sclerotium and soil samples, as well as pure cultures, using simplex and multiplex qPCRs. This multiplex assay could be helpful in detecting and quantifying specific species of Sclerotinia, and therefore, may be valuable for disease diagnosis, forecasting, and management.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.8
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• pp.3189-3194
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• 2015

Background: To explore the expression of TS, RRM, ERCC1, TUBB3 and STMN1 genes in the tissues of patients with non-small cell lung cancer (NSCLC) and its significance in guiding the postoperative adjuvant chemotherapy. Materials and Methods: Real time polymerase chain reaction (PCR) was applied to detect the expression of TS, RRM, ERCC1, TUBB3 and STMN1 genes in the tissues of NSCLC patients so as to analyze the relationship between the expression of each gene and the clinical characteristics and to guide the postoperative individualized chemotherapy according to the detection results of NSCLC patients. Results: Expression of TS gene was evidently higher in patients with adenocarcinoma than those with non-adenocarcinoma (P=0.013) and so was the expression of ERCC1 (P=0.003). The expression of TUBB3 gene was obviously higher in NSCLC patients in phases I/II and IV than those in phase III ($P_1=0.021$; $P_2=0.004$), and it was also markedly higher in patients without lymph node metastasis than those with (P=0.008). The expression of STMN1 gene was apparently higher in patients in phase I/II than those in phase IV (P=0.002). There was no significant difference between the rest gene expression and the clinical characteristics of NSCLC patients (P>0.05). Additionally, the diseasefree survival (DFS) was significantly longer in patients receiving gene detections than those without (P=0.021). Conclusions: The selection of chemotherapeutic protocols based singly on patients' clinical characteristics has certain blindness. However, the detection of tumor-susceptible genes can guide the postoperative adjuvant chemotherapy and prolong the DFS of NSCLC patients.

• Journal of Genetic Medicine
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• v.21 no.1
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• pp.22-30
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• 2024

Purpose: Neurofibromatosis 1 (NF1) is one of the most common autosomal dominant diseases caused by heterozygous mutation in the NF1 gene. Mutation detection is complex owing to the large size of the NF1 gene, the presence of a high number of partial pseudogenes, and the great variety of mutations. We aimed to study the mutation spectrum of NF1 gene in Korean patients with NF1. Materials and Methods: We have analyzed total 69 unrelated patients who were clinically diagnosed with NF1. PCR and sequencing of the NF1 gene was performed in all unrelated index patients. Additionally, multiplex ligation-dependent probe amplification (MLPA) test of the NF1 and SPRED1 gene analysis (sequencing and MLPA test) were performed in patients with negative results from NF1 gene sequencing analysis. Results: Fifty-five different variants were identified in 60 individuals, including six novel variants. The mutations included 36 single base substitutions (15 missense and 21 nonsense), eight splicing mutations, 13 small insertion or deletions, and three gross deletions. Most pathogenic variants were unique. The mutations were evenly distributed across exon one through 58 of NF1, and no mutational hot spots were found. When fulfilling the National Institutes of Health criterion for the clinical diagnosis of NF1, the detection rate was 84.1%. Cafe-au-lait macules were observed in all patients with NF1 mutations. There is no clear relationship between specific mutations and clinical features. Conclusion: This study revealed a wide spectrum and genetic basis of patients with NF1 in Korea. Our results aim to contribute genetic management and counseling.

• Asian-Australasian Journal of Animal Sciences
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• v.11 no.5
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• pp.498-502
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• 1998

The present study was designed, fIrst to develop the new methodology to measure the bioluminescence activity easily in live developing bovine embryos by photoncounting, and secondly to compare the expression efficiency of four luciferase reporter genes in bovine embryos at four- to 16-cell stages. In experiment 1, equimolar pSVlacZ and pSVEluc were microinjected into the pronucleus of fertilized bovine oocytes. At 2 days after micro injection, bioluminescence activity of these embryos was measured by photoncounting with a luminometer for 1 min, and lacZ gene expression in the same embryos was assayed by X-gal staining. All the luciferase-positive oocytes showed some bacterial ${\beta}$-galactosidase activity irrespective of the intensity. In experiment 2, four firefly luciferase genes (pTKEluc, pTK6WEluc, pSVEluc and pMiwluc) were introduced by micro injection, and the injected embryos were cultured for the following 2 days. Detection of the luciferase gene expression was done by photoncounting at 5 to 55 min. Over the measurement period, the luciferase activity was almost constant irrespective of the transgenes microinjected. The luciferase activity and expression efficiency at 2 days after microinjection were not significantly affected by the difference in the microinjected transgenes. The present results demonstrated that the bioluminescence activity in live developing bovine embryos could be measured quickly by photoncounting.

• Journal of Microbiology
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• v.38 no.3
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• pp.183-186
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• 2000

Several types of bioluminescent reporter strains have been developed for the detection and monitoring of pollutant aromatics contaminating the environment. In this study, a bioluminescent reporter strain, E. coli SHP3, was constructed by fusing the luc gene of firefly luciferase with the promoter of pcbC responsible for the meta-cleavage of aromatic hydrocarbons. the bioluminescence expressed by the luc gene in the reporter was well triggered by the promoter when it was exposed to 2,3-dihydroxybiphenyI (2,3-DHBP) at 0.5 to 1 mM concentrations. The bioluminescent response was more extensive when the reporter strain was exposed to 5 mM catechol and 2 mM 4-chlorocatechol. These different types of bioluminescent responses by E. coli SHP3 appeared to be characterized by the nature of the aromatics to stress. Since E. coli SHP3 responded to 2,3-DHBP quite sensitively, this reporter strain could be applied for detecting some catecholic pollutants.

• Journal of Environmental Health Sciences
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• v.31 no.1
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• pp.23-30
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• 2005

Staphylococcus aureus is one of the important pathogenic agents, which are related to the hygienic condition. This study performed for the detection of Staphylococcus aureus and screening staphylococcal enterotoxin a, b, c genes in strains isolated from the environment for production of non-pasteurized strawberry juice. A total of 44 samples were collected from utensils, machinery, employees, raw materials, and strawberry juices in 3 strawberry juice shops in Jinju, western Gyeongnam. The isolation rate of Staphylococcus aureus was 26%. Specially Staphylococcus aureus was frequently isolated from employee's hands, strawberry and strawberry juices. The sea, seb, and sec genes were also investigated by polymerase chain reaction (PCR). One hundred and 55% of each isolate had found sea gene and seb gene, respectively. However, sec gene was not detected anywhere. To prevent food-borne disease associated with juice, the accomplishment of HACCP to be more efficient and systematic is necessary.