Development and application of real-time PCR for specific detection of Lepeophtheirus salmonis and Caligus elongatus larvae in Scottish plankton samples
Bibliographic record
Abstract
Lepeophtheirus salmonis and Caligus elongatus are important parasites of wild and cultured salmonids in the Northern Hemisphere. These species, generically referred to as sea lice, are estimated to cost the Scottish aquaculture industry in excess of pound 25 million per annum. There is great interest in countries such as Ireland, Scotland, Norway and Canada to sample sea lice larvae in their natural environment in order to understand lice larvae distribution and improve parasite control. Microscopy is currently relied on for use in the routine identification of sea lice larvae in plankton samples. This method is, however, limited by its time-consuming nature and requirement for highly skilled personnel. The development of alternative methods for the detection of sea lice larvae which might be used to complement and support microscopic examinations of environmental samples is thus desirable. In this study, a genetic method utilising a real-time PCR Taqman-MGB probe-based assay targeting the mitochondrial cytochrome oxidase I (mtCOI) gene was developed, which allowed species-specific detection of L. salmonis and C. elongatus larvae from unsorted natural and spiked plankton samples. Real-time PCR is a rapid, sensitive, highly specific and potentially quantitative technique. This study demonstrated its suitability for the routine identification of L. salmonis and C. elongatus in mixed plankton samples. The real-time PCR assay developed has considerable potential for use in complementing, supporting and reducing reliance on time-consuming conventional microscopic examination for the specific identification of sea lice larvae in plankton samples.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".