Detection of the Genus Phytophthora and the Species Phytophthora nicotianae by LAMP with a QProbe

Phytophthora is an oomycete genus with worldwide distribution, and many of its species cause destructive diseases. In Japan, Phytophthora species are listed as quarantine organisms with the exception of Phytophthora nicotianae. For effective quarantine control, we designed a Phytophthora genus-specific loop-mediated isothermal amplification (LAMP) primer set and a P. nicotianae species-specific quenching probe (QProbe) to establish a simultaneous LAMP-based detection method. We confirmed the specificity of the genus-specific primers, and all 161 taxa were detected. No other species in the closely related genera Pythium and Phytopythium gave positive results with the exception of two species, Phytopythium delawarense and Phytopythium fagopyri. These two species gave inconsistent results. We used annealing curve analysis with the QProbe to demonstrate that P. nicotianae could be distinguished from other species. DNA from inoculated and naturally infected plants was extracted using a time-saving extraction kit and subjected to the simultaneous detection method. We confirmed that all Phytophthora DNAs in the plant samples were detected, and P. nicotianae was specifically identified. This simultaneous detection method will make quarantine inspections faster and easier.

Loop-mediated isothermal amplification–fluorescent loop primer assay for the genotyping of a single nucleotide polymorphism at position 2254 in the viral DNA polymerase gene of equid alphaherpesvirus 1

We developed a loop-mediated isothermal amplification (LAMP)–fluorescent loop primer (FLP) assay for genotyping the A/G2254 single nucleotide polymorphism (SNP) in the viral DNA polymerase gene of species Equid alphaherpesvirus 1 (EHV-1), which is associated with the neuropathogenic potential of this virus. In addition to the use of regular LAMP primers to amplify the target region, a 5’-FAM–labeled backward loop primer (FLB) and 3’-dabcyl–labeled quencher probe (QP) were designed for annealing curve analysis of the amplification product. The QP, which contacts the FLB, is located at the SNP site and has the A2254 allele. LAMP reactions were performed at 63°C for 40 min, and the subsequent annealing curve analyses were accomplished within 20 min. The LAMP-FLP assay could clearly differentiate A2254 and G2254 genotypes according to the difference in the annealing temperature of the QP between the 2 genotypes. Good agreement between the LAMP-FLP and the real-time PCR for genotyping of this SNP was observed in the detection of EHV-1 in equine clinical samples. The newly developed assay is a simple and rapid method for detecting and differentiating EHV-1 strains with A2254 and G2254 polymorphisms and would be suitable for clinical use.

The Influence of Irradiation Temperature on U.V. Induced Defect Creation in Dry Silica

ABSTRACTElectron spin resonance measurements have been carried out on samples of Suprasil Wl (dry silica) subjected to ultraviolet laser radiation (λ = 248 nm, E = 5 eV/photon). Studies have been made for fixed irradiation temperature (room) variable accumulated ultraviolet dose and fixed accumulated dose (3000 J/cm2) at various irradiation temperatures in the range 110 K to 335 K. Three principal defect centers are observed. Non-bridging oxygen hole centers are created at all temperatures in the range studied with slightly higher efficiency at room temperature (ration 300 K/150 K ∼ 2.5). Comparison of the dose dependent growth curve of the 4.8 eV absorption and its isochronal annealing curve with those for the oxygen hole center clearly identify the origin of the absorption band with this defect. A threshold temperature ∼ 200 K is found for oxygen vacancy creation consistent with results on single crystalline quartz. Post irradiation annealing at 593 K eliminates the vacancy centers and the peroxy radical resonance appears. Its growth as a function of accumulated ultraviolet dose and irradiation temperature supports the hypothesis that peroxy radicals form by the trapping of diffusing, molecular oxygen at the oxygen vacancy center.