Dead or Alive, that Is the Question: Development and Assessment of Molecular <i>Synchytrium endobioticum</i> Viability Tests
Bibliographic record
Abstract
Potato wart disease caused by the obligate biotrophic fungus Synchytrium endobioticum is a devastating disease that can result in significant crop losses. Resting spores of this pathogen can remain viable and infectious in soil for decades. The detection of viable resting spores using conventional methods such as bioassays and direct microscopic examination are challenging and time-consuming and require specific expertise and facilities. Molecular methods, such as real-time PCR, have been shown to be effective in detecting the presence of S. endobioticum DNA in soil samples but cannot differentiate between viable and nonviable spores. In this paper, we present three novel mRNA-based molecular tests to potentially detect viable S. endobioticum resting spores. The tests are specific to the transcribed mRNA and do not detect the genomic DNA of the target genes. We demonstrate the analytical sensitivity using synthetic constructs of the target mRNAs. The tests were found to be able to repeatedly detect 10 target copies per reaction. Soils and waste of potato processing industries free from S. endobioticum were used to assess the exclusivity of the tests. The biological relevance of mRNA detection was determined in the context of replicated bioassays. Applications of the tests to facilitate collection management, assessment of the effects of treatments on presumed viability of S. endobioticum resting spores, and the potential use in descheduling of previously infested plots are discussed. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".