PDA Technical Glossary
PDA Technical Reports are highly valued membership benefits because they offer expert guidance and opinions on important scientific and regulatory topics and are used as essential references by industry and regulatory authorities around the world. These reports include terms which explain the material and enhance the reader’s understanding.
The database presented here includes the glossary terms from all current technical reports. The database is searchable by keyword, topic, or by technical report. Each definition provided includes a link to the source technical report within the PDA Technical Report Portal.
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Amplicon
A segment of double stranded DNA formed as the product of polymerase chain reaction or other amplification based techniques such as TMA or NASBA. (TR50)
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CFU: Genome Copy Ratio
The relationship between the number of colony forming units counted on solid media and the number of genome copies measured using a method suitable for quantitative assessment of genomic DNA. (TR50)
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Color Changing Unit (CCU)
The quantity of mycoplasma contained in the highest dilution of a test article that produces a color change in a pH-sensitive liquid medium (typically containing phenol red) within a specified time of incubation, used for end-point determination of growth. (TR50)
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Comparability Study
An assessment of the similarities between the critical parameters and output results of two or more separate processes or methods. (TR50)
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Endpoint PCR
A classical PCR method based on repeated cycling of the reaction mixture between two or three temperatures (denaturing, annealing, and extension) with detection of the amplified product after reaction completion (e.g., by agarose gel electrophoresis). (TR50)
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Extraction Control
A known test article processed with a nucleic acid extraction procedure in order to ensure the proper extraction of nucleic acid. (TR50)
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Extraction Recovery
The efficiency of extraction of target analyte from a test matrix. It is usually measured as ratio (percentage) of analyte amount extracted from the matrix to that originally present in the matrix before extraction. (TR50)
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Fastidious strain (isolate)
A population of microorganisms having complex nutritional requirements and thus difficult to cultivate. (TR50)
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Genome Copy (GC)
An amount of nucleic acid equivalent to the genetic complement present in the genome of a single microorganism. (TR50)
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Hybridization
The formation of a double-stranded complex of complementary strands of nucleic acids (e.g., a primer and single-stranded DNA or RNA) (TR50)
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Magnetic Capture Hybridization (MCH)
A purification method based on sequence-specific hybridization of labeled nucleic acid probes with targeted regions of test article nucleic acids, followed by magnetic bead capture. (TR50)
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Matrix Spike Control
An internal control in which an amplifiable amount of nucleic acid is added to a test article to determine inhibition of the PCR. This addition is usually performed pre-extraction and should provide a weak signal 100% of the time. Also known as “interference control”. (TR50)
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Mollicutes
A class of bacteria which lack a cell wall. Mollicutes are small, typically about 0.1-0.5 &mum in size, and vary in form (trivial name: mycoplasma) (TR50)
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Negative Control
A test article used to assess the performance of an assay in the known absence of a targeted microorganism or nucleic acid. Negative controls are used to minimize a risk of false positive results, which could occur due to non-specific signals. (TR50)
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Plasmid
An extra-chromosomal DNA molecule in bacteria which is capable of replicating independently of the host chromosomal DNA. Plasmids are often used as positive controls for NAT assays. (TR50)
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Specificity
The ability of an analytical procedure to accurately measure or detect a target analyte in the presence of other components in the sample matrix. (TR50) The ability to assess unequivocally the analyte in the presence of components that may be expected to be present. Typically these might include impurities, degradants, matrix, etc. Lack of specificity of an individual analytical procedure may be compensated by other supporting analytical procedure(s). (TR57) The ability to detect a range of microorganisms, which demonstrate that the method is fit for its intended use. (TR33)
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Toll-like Receptor (TLR)
A class of single membrane-spanning non-catalytic receptors that recognize structurally conserved molecules derived from microbes. They can activate immune cell responses when microbes have breached physical barriers such as the skin or intestinal tract mucosa. (TR50)
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Touchdown PCR
A technique to reduce appearance of non-specific amplicons in PCR reactions. The earliest cycles of a touchdown PCR method have high annealing temperatures. The annealing temperature is decreased in increments for subsequent cycles until a fixed point is reached. (TR50)
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Transcription-Mediated Amplification (TMA)
An isothermal NAT method that can amplify RNA or DNA targets a billion-fold in less than one hour. TMA technology uses two primers and two enzymes: RNA polymerase and reverse transcriptase. (TR50)