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

Plant Disease ◽  
2020 ◽  
Vol 104 (9) ◽  
pp. 2469-2480
Author(s):  
Ayaka Hieno ◽  
Mingzhu Li ◽  
Auliana Afandi ◽  
Kayoko Otsubo ◽  
Haruhisa Suga ◽  
...  
Keyword(s):  
Detection Method ◽  
Simultaneous Detection ◽  
Phytophthora Species ◽  
Phytophthora Nicotianae ◽  
Time Saving ◽  
Worldwide Distribution ◽  
Quenching Probe ◽  
Species Specific ◽  
Annealing Curve ◽  
Positive Results

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.

scholarly journals Natural Hybrids of Phytophthora nicotianae and Phytophthora cactorum Demonstrated by Isozyme Analysis and Random Amplified Polymorphic DNA

1998 ◽  
Vol 88 (9) ◽  
pp. 922-929 ◽  
Author(s):  
Willem A. Man in 't Veld ◽  
Wil J. Veenbaas-Rijks ◽  
Elena Ilieva ◽  
Arthur W. A. M. de Cock ◽  
Peter J. M. Bonants ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Restriction Enzymes ◽  
Phytophthora Species ◽  
Phytophthora Nicotianae ◽  
Isozyme Analysis ◽  
Maximum Temperature ◽  
Banding Patterns ◽  
The One ◽  
Species Specific ◽  
Putative Locus

Three similar isolates of Phytophthora (Phytophthora sp-h) were obtained from diseased Spathiphyllum and Primula plants. Cultural characteristics did not fit any known description of Phytophthora species. The Phytophthora sp-h isolates are papillate, are homothallic, possess 80 to 86% amphigynous antheridia, and have a maximum temperature for growth of 36.5°C. Isozyme analysis of the Phytophthora sp-h isolates revealed a three-banded pattern with malic enzyme and a three-banded pattern with malate dehydrogenase on the second putative locus. The fastest band at both enzyme loci comigrated with the single P. nicotianae band, the slowest band comigrated with the single P. cactorum (and also P. pseudotsugae) band, and one band in between was concluded to represent the heterodimeric isozyme. The random amplified polymorphic DNA patterns of the Phytophthora sp-h isolates almost exclusively consisted of bands that were also present in either P. nicotianae or P. cactorum. Southern hybridization showed that bands specific for P. nicotianae were present as comigrating bands in the Phytophthora sp-h isolates. The same was found for species-specific bands of P. cactorum. It is concluded that the three Phytophthora sp-h isolates represent interspecific hybrids, P. nicotianae being the one parent and P. cactorum the other. Analysis of mito-chondrial DNA with restriction enzymes revealed banding patterns in all the Phytophthora sp-h isolates identical with those of P. nicotianae, confirming that indeed P. nicotianae was one of the parents.

Species Specific Immunoassays to Measure Blood Platelet and Coagulation Activation in the Rat

1996 ◽  
Vol 76 (06) ◽  
pp. 1090-1095 ◽  
Author(s):  
C Ravanat ◽  
M Freund ◽  
S Schuhler ◽  
P Grunert ◽  
L Meyer ◽  
...  
Keyword(s):  
Antithrombin Iii ◽  
Plasma Concentrations ◽  
Simultaneous Detection ◽  
Blood Platelet ◽  
Coagulation Activation ◽  
Platelet Factor ◽  
Prethrombotic State ◽  
Low Levels ◽  
Species Specific ◽  
Higher Sensitivity

SummaryThe purpose of this study was to develop specific and sensitive immunoassays to detect early indices of hypercoagulability in the rat. Rat platelet factor 4 (rPF4) and rat fibrinopeptide A (rFPA) assays, tools for the detection of activation of platelets and coagulation respectively, were designed using antibodies raised against purified rPF4 and against synthetic rFPA. The relevance of these new assays and of the commercially available ELISA kit for thrombin-antithrombin III (TAT) complexes was demonstrated in a rat model of a prethrombotic state induced by intravenous infusion of varying doses of thromboplastin (90 to 2400 μl/kg/h). In this model, the immunoassays allowed simultaneous detection of low levels of rFPA and rPF4 which were correlated with fibrinogen and platelet consumption and TAT generation and further proved to be of higher sensitivity than the classical methods of platelet count or measurement of fibrinogen levels. Plasma concentrations of rFPA, rPF4 and TAT were dependent on infusion time and thromboplastin dose, while hirudin (1 mg/kg) prevented their appearance. Thus the new specific immunoassays for rPF4 and rFPA and the commercial human TAT assay represent useful tools for pathophysiological studies or the screening of antithrombotic drugs in rats.

scholarly journals A New Multiplex Real-Time RT-PCR for Simultaneous Detection and Differentiation of Avian Bornaviruses

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1358
Author(s):  
Brigitte Sigrist ◽  
Jessica Geers ◽  
Sarah Albini ◽  
Dennis Rubbenstroth ◽  
Nina Wolfrum
Keyword(s):  
Real Time ◽  
Simultaneous Detection ◽  
Epidemiological Studies ◽  
Virus Species ◽  
Rt Pcr ◽  
P Gene ◽  
Field Samples ◽  
Causative Agents ◽  
Species Specific ◽  
Proventricular Dilatation Disease

Avian bornaviruses were first described in 2008 as the causative agents of proventricular dilatation disease (PDD) in parrots and their relatives (Psittaciformes). To date, 15 genetically highly diverse avian bornaviruses covering at least five viral species have been discovered in different bird orders. Currently, the primary diagnostic tool is the detection of viral RNA by conventional or real-time RT-PCR (rRT-PCR). One of the drawbacks of this is the usage of either specific assays, allowing the detection of one particular virus, or of assays with a broad detection spectrum, which, however, do not allow for the simultaneous specification of the detected virus. To facilitate the simultaneous detection and specification of avian bornaviruses, a multiplex real-time RT-PCR assay was developed. Whole-genome sequences of various bornaviruses were aligned. Primers were designed to recognize conserved regions within the overlapping X/P gene and probes were selected to detect virus species-specific regions within the target region. The optimization of the assay resulted in the sensitive and specific detection of bornaviruses of Psittaciformes, Passeriformes, and aquatic birds. Finally, the new rRT-PCR was successfully employed to detect avian bornaviruses in field samples from various avian species. This assay will serve as powerful tool in epidemiological studies and will improve avian bornavirus detection.

SEROLOGICAL AND MOLECULAR EVALUATION OF MIGRATORY TRICHINELLA SPIRALIS LARVAE IN BLOOD OF HUMANS IN KADUNA METROPOLIS, NIGERIA

2021 ◽  
Vol 4 (4) ◽  
pp. 281-289
Author(s):  
Paul Isaac Ojodale ◽  
Helen Ileigo Inabo ◽  
Elijah Ekah Ella ◽  
Oluyinka Oluseyi Okubanjo
Keyword(s):  
Trichinella Spiralis ◽  
Enzyme Linked Immunosorbent Assay ◽  
Seroprevalence Rate ◽  
Base Pairs ◽  
Worldwide Distribution ◽  
Food Borne ◽  
Atp6 Gene ◽  
Amplicon Size ◽  
Polymerase Chain ◽  
Species Specific

Trichinellosis is an important food-borne zoonotic disease with public health implications and a worldwide distribution. In this study, Polymerase Chain Reaction (PCR) procedure using species specific ATP6 primers was used to detect the presence of migratory Trichinella spiralis larval mitochondrial ATP6 synthase F0 subunit (ATP6) gene, after detection of antibodies to Trichinella excretory-secretory (E/S) antigen using Enzyme-linked Immunosorbent Assay (ELISA), in blood of humans in Kaduna metropolis, Nigeria. The sera of 210 participants were tested for antibodies to Trichinella E/S antigen. Overall seroprevalence rate of 39% (82/210) was recorded using ELISA. Out of the 9 ELISA samples selected randomly, PCR detected migratory Trichinella spiralis larval ATP6 gene in 4 (44.4%) at the amplicon size of 250 base pairs using the whole blood of the participants.  The 9 samples comprised 7 seropositive and 2 seronegative. The bands at lanes 1, 2, 3 and 4 were positive for ATP6 while lanes 5,6,7,8 and 9 were negative for ATP6.  Lanes 4 and 5 were ELISA negative for anti-Trichinella antibodies. One in 5 of the 128 ELISA negative samples was positive for ATP6 representing a 25.6% prevalence rate by extrapolation.  PCR using ATP6 gene as a genetic marker is valuable for the detection of T. spiralis migratory larvae in blood samples of humans and consequently the early diagnosis of trichinellosis in humans.

scholarly journals Research on breakpoint area detection of computer communication network transmission data based on cloud framework

2021 ◽  
Vol 2083 (4) ◽  
pp. 042045
Author(s):  
Shichuang Zheng ◽  
Jiajun Li ◽  
Shuai Chen ◽  
Yujia Liang ◽  
Jiangtao Lin
Keyword(s):  
Communication Network ◽  
Detection Method ◽  
Distribution Characteristics ◽  
Time Saving ◽  
Computer Communication ◽  
Transmission Data ◽  
Cloud Framework ◽  
Breakpoint Detection ◽  
Network Transmission ◽  
Computer Communication Network

Abstract Traditional detection method of data breakpoint in computer communication network has some disadvantages, such as time consuming, etc. Firstly, the data of computer transmission breakpoints are stored based on cloud framework, and the density distribution characteristics of the region are extracted according to the breakpoint data. Then the optimal data breakpoint detection path is selected. Finally, the similarity of each data breakpoint is detected by the computer, so that the detection of data breakpoints is realized by computer. After experiments, the data breakpoint detection is realized, the results show that the designed method can detect data breakpoints accurately, which is time-saving and has a certain significance of popularization.

Experimental Methods

2007 ◽  
Author(s):  
Robert B. Jordan
Keyword(s):  
Kinetic Study ◽  
Detection Method ◽  
Kinetic Method ◽  
Critical Factor ◽  
Spectroscopic Properties ◽  
Product Formation ◽  
Visible Range ◽  
Time Range ◽  
Low Sensitivity ◽  
Species Specific

A kinetic study generally proceeds after the reactants, products and stoichiometry of the reaction have been satisfactorily characterized. The more one knows about the chemistry of the reaction, the better the conclusions that one can draw from a kinetic study. The discussion here describes techniques often used in inorganic studies, emphasizes their time range and general area of applicability and gives some examples of their use. Further details can be found in other sources. Any experimental kinetic method must somehow monitor change of concentration with time. Many studies are done under pseudo-first-order conditions, and then one must monitor the deficient reactant or product(s) because the other species undergo small changes in concentration. The kinetic method(s) of choice often will be dictated by the time scale of the reaction. The detection method(s) will be determined by the spectroscopic properties of the species to be monitored. The efficient use of materials can be a significant factor in the choice of method because a kinetic study generally involves a number of runs at different concentrations and temperatures, and conservation of difficult to prepare or expensive reagents may be a critical factor. The detection method should be as species specific as possible, and ideally one would like to measure both reactant disappearance and product formation. The method must not be subject to interference from other reactants and should be applicable under a wide range of concentration conditions so that the rate law can be fully explored. Often there is a practical trade-off between specificity, sensitivity and reaction time. For example, NMR is quite specific but rather slow and has relatively low sensitivity, unless the system allows time for signal accumulation. Spectrophotometry in the UV and visible range often has good sensitivity and speed, but the specificity may be poor because absorbance bands are broad and intermediates may have chromophoric properties similar to those of the reactant and/or product. Vibrational Spectrophotometry can be better if the IR bands are sharp, as in the case of metal carbonyls, but the solvent must be chosen to provide an appropriate spectral window.

scholarly journals Application of InDel markers based on the chloroplast genome sequences for authentication and traceability of tartary and common buckwheat

2017 ◽  
Vol 35 (No. 2) ◽  
pp. 122-130 ◽  
Author(s):  
Cho Kwang-Soo ◽  
Hong Su-Young ◽  
Yun Bong-Kyoung ◽  
Won Hong-Sik ◽  
Yoon Young-Ho ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Detection Method ◽  
Processed Foods ◽  
Common Buckwheat ◽  
Genome Sequences ◽  
Specific Pcr ◽  
Indel Markers ◽  
Specificity And Sensitivity ◽  
Species Specific ◽  
Qualitative Pcr

A reliable, qualitative PCR-based detection method for the traceability and authentication of common and Tartary buckwheat was developed. Five InDel markers developed from chloroplast genome variation between the two species were applied for 96 buckwheat accessions and all accessions were easily differentiated as Tartary and common buckwheat using these markers. We also determined the sample detection limit by PCR and qPCR as 0.001 and 0.02 ng/µl, respectively. InDel markers could detect the mixture of two species flour up to 10% contamination. InDel markers were also applied to processed foods such as noodles and tea, and we found that species-specific PCR bands could be used to identify buckwheat even after processing. Hence, these InDel markers are simple with higher specificity and sensitivity and are reliable for the authentication of buckwheat processed foods.

scholarly journals Detection of Trypanosoma cruzi and Trypanosoma rangeli Infection by Duplex PCR Assay Based on Telomeric Sequences

2003 ◽  
Vol 10 (5) ◽  
pp. 775-779 ◽  
Author(s):  
Miguel Angel Chiurillo ◽  
Gladys Crisante ◽  
Agustina Rojas ◽  
Andreina Peralta ◽  
Manuel Dias ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Human Subjects ◽  
Simultaneous Detection ◽  
Duplex Pcr ◽  
Trypanosoma Rangeli ◽  
Pcr Assay ◽  
Telomeric Sequences ◽  
Species Specific ◽  
Duplex Pcr Assay ◽  
Reduviid Bugs

ABSTRACT We used the species specificity and repetitious nature of subtelomeric kinetoplastida sequences to generate a duplex PCR assay for the simultaneous detection of Trypanosoma cruzi and Trypanosoma rangeli in experimentally and naturally infected triatomine (Reduviid) bugs and in infected human subjects. The assay was species specific and was capable of detecting 1/20th of T. cruzi and 1/4th of T. rangeli cell equivalents without complementary hybridization. In addition, the PCR-based assay was robust enough for direct application to difficult biological samples such as Reduviid feces or guts and was capable of recognizing all T. cruzi and T. rangeli strains and lineages. Because the assay primers amplify entirely different target sequences, no reaction interference was observed, facilitating future adaptation of this assay to an automated format.

Simultaneous detection ofAureliaandChrysaorascyphozoan jellyfish on a DNA microarray

2009 ◽  
Vol 90 (6) ◽  
pp. 1111-1117 ◽  
Author(s):  
Jang-Seu Ki ◽  
Dae-Sik Hwang ◽  
Jae-Seong Lee
Keyword(s):  
Dna Microarray ◽  
Simultaneous Detection ◽  
Dna Chip ◽  
Coi Gene ◽  
Low Density ◽  
Sequence Comparisons ◽  
Mitochondrial Coi ◽  
Pcr Products ◽  
Jellyfish Species ◽  
Species Specific

To demonstrate the effectiveness of microarrays for the detection of jellyfish, we developed a low density DNA chip based on the mitochondrial COI gene sequences of scyphozoans (jellyfish). We designed species-specific oligonucleotide probes by sequence comparisons between scyphozoans and other cnidarians such as hydrozoans and anthozoans. Each amine-labelled capture probe was arrayed onto a silylated slide. PCR products of the COI gene were hybridized to the DNA microarray that contained COI consensus sequences. We tested the ability of the DNA chip to discriminate between species from the generaAureliaandChrysaorabased on samples of both species from the polyp and ephyra stages. The array produced unique hybridization patterns for each of the two tested jellyfish species. Furthermore, we were able to simultaneously detect individual jellyfish species from mixtures of these two different species in the laboratory and from environmental samples. These results show that the low density DNA chip that we designed can be used as a technical platform for parallel molecular detection of various jellyfish species.

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