Study of the distribution of Megasphaera micronuciformis in oral cavities of the Japanese by species-specific polymerase chain reaction (PCR) assay

Phytophthora nicotianae is a common and destructive pathogen of numerous ornamental, agronomic, and horticultural crops such as tobacco, tomato, and citrus. We have developed a species-specific polymerase chain reaction (PCR) assay for rapid and accurate detection of this pathogen in irrigation water, a primary source of inoculum and an efficient means of propagule dissemination. This PCR assay consists of a pair of species-specific primers (PN), customization of a commercial soil DNA extraction kit for purification of DNA from propagules in irrigation water, and efficient PCR protocols for primer tests and sample detection. The PN primers proved adequately specific for P. nicotianae in evaluations with 131 isolates of P. nicotianae, 102 isolates from 15 other species of Phytophthora, and 64 isolates from a variety of other oomycetes, true fungi, and bacteria. These isolates originated from a wide range of host plants, three substrates (plant tissue, soil, and irrigation water), and numerous geographic locations. The detection sensitivity is between 80 and 800 fg DNA/μl. The assay detected the pathogen in naturally infested water samples from Virginia and South Carolina nurseries more rapidly and accurately than standard isolation methods. Use of this PCR assay can assist growers in making timely disease management decisions with confidence.

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Species specific polymerase chain reaction (PCR) assay for identification of pig (Sus domesticus) meat

AFRICAN JOURNAL OF BIOTECHNOLOGY ◽

10.5897/ajb12.1753 ◽

2012 ◽

Vol 11 (89) ◽

pp. 15590-15595 ◽

Cited By ~ 6

Author(s):

Kumar Arun ◽

Ranjan Kumar Rajiv ◽

Deo Sharma Brahma ◽

Kumar Mendiratta Sanjod ◽

Sharma Deepak ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Chain Reaction ◽

Pcr Assay ◽

Specific Polymerase Chain Reaction ◽

Polymerase Chain ◽

Species Specific ◽

Sus Domesticus

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Evaluation of the Brucella Abortus Species–Specific Polymerase Chain Reaction Assay, an Improved Version of the Brucella AMOS Polymerase Chain Reaction Assay for Cattle

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063870301500413 ◽

2003 ◽

Vol 15 (4) ◽

pp. 374-378 ◽

Cited By ~ 22

Author(s):

Betsy J. Bricker ◽

Darla R. Ewalt ◽

Steven C. Olsen ◽

Allen E. Jensen

Keyword(s):

Polymerase Chain Reaction ◽

Brucella Abortus ◽

Polymerase Chain Reaction Assay ◽

Chain Reaction ◽

Pcr Assay ◽

Diagnostic Pcr ◽

Specific Polymerase Chain Reaction ◽

Significant Difference ◽

Polymerase Chain ◽

Species Specific

In a blind test, 344 samples representing 80 bacterial isolates were analyzed by the Brucella abortus species–specific polymerase chain reaction (BaSS PCR) assay for the identification and discrimination of B. abortus field strains (wild-type biovars 1, 2, and 4) from 1) B. abortus vaccine strains, 2) other Brucella species, and 3) non- Brucella bacteria. Identical samples were tested in 2 laboratories. Half the samples were fully viable, and half were bacteria that had been killed by methanol fixation. The results in 1 laboratory correctly identified 100% of the samples, resulting in a predictive value of 100% for all categories and 100% sensitivity and specificity under the prescribed conditions. The second laboratory misidentified 31 samples, resulting in a range of 66.7–100% sensitivity, 93.2–99.7% specificity, and 77.3–98.2% predictive values depending on the category. There was no significant difference in viable versus fixed bacteria for either laboratory. Subsequent review of the protocol indicated that contamination was the likely cause of 26 of the 31 erroneous identifications. The results show that the BaSS PCR assay has the potential to be a very reliable screening tool for B. abortus identification. However, the data also provide a cautionary reminder of the importance of preventing contamination in diagnostic PCR.

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Routine identification of four sympatric species of calanoid copepods Pseudocalanus spp. in the Atlantic Arctic using a species-specific polymerase chain reaction

Journal of Oceanological Research ◽

10.29006/1564-2291.jor-2020.48(1).4 ◽

2020 ◽

Vol 48 (1) ◽

pp. 62-72

Author(s):

E. A. Ershova

Keyword(s):

Polymerase Chain Reaction ◽

Life Cycles ◽

The Arctic ◽

Relative Distribution ◽

Chain Reaction ◽

Specific Polymerase Chain Reaction ◽

Routine Identification ◽

Polymerase Chain ◽

Species Specific ◽

Plankton Communities

Сalanoid copepods of the genus Pseudocalanus play an important role in the plankton communities of the Arctic and boreal seas, often dominating in numbers and constituting a significant proportion of the biomass of zooplankton. Despite their high presence and significance in the shelf plankton communities, species-specific studies of the biology of these are significantly hampered by extremely small morphological differences between them, especially at the juvenile stages, at which they are virtually indistinguishable. In this paper, we describe a new, routine and low-cost molecular method for identifying all Pseudocalanus species found in the Atlantic sector of the Arctic: the Arctic P. acuspes, P. minutus and the boreal P. moultoni and P. elongatus, and apply it to describe the relative distribution of these species in four locations of the Arctic and sub-Arctic. With this method, species-specific polymerase chain reaction (ssPCR), mass identification of individuals of any developmental stage, including nauplii, is possible. This method can serve as an excellent tool for studying the species-specific biology of this group, describing their life cycles, as well as monitoring changes in Arctic marine ecosystems under the influence of changing climate.

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