Detection of the amphibian pathogen Batrachochytrium dendrobatidis on spadefoots in the Kamloops region
Bibliographic record
Abstract
Batrachochytrium dendrobatidis is a species of chytrid fungus responsible for the decline and extinction of amphibian populations worldwide (Longcore 1999 and others). Recently, B. dendrobatidis has been detected on western toads (Bufo boreas) in southwestern British Columbia (Deguise & Richardson 2009) and has therefore become a concern for conservationists across the province. Chytrid DNA can be extracted from tissue samples, skin swabs, and water bodies and subsequently detected using real time PCR techniques. It is currently unknown whether the chytrid fungus is affecting amphibian populations in the Kamloops area. This project aimed to first validate an effective real time PCR assay for detecting the presence of the amphibian pathogen B. dendrobatidis, and second to employ this real time PCR assay to detect B. dendrobatidis on experimental samples collected in the Kamloops region.\nSpecifically, spadefoots were captured during the summer of 2013 from the New Afton mining site located south of Kamloops, BC. A total of 78 spadefoots were captured, swabbed, and subsequently weighed, measured and released. Parameters for optimizing an effective real time PCR assay were tested to detect B. dendrobatidis in experimental samples; initially a Taqman assay was tried, but due to a lack of success, a SYBR Green assay was used. DNA was extracted from all samples and 30 of these samples were tested for B. dendrobatidis using the SYBR Green assay and gel electrophoresis.\nB. dendrobatidis DNA was not detected in any of the 30 experimental samples. Melt curve analysis indicated the presence of multiple PCR products, products which were observed by gel electrophoresis at lengths less than 150 base pairs. It is possible that non-specific primer binding occurred, or that primer dimers formed, at low template DNA concentrations as these bands were not observed above 42 standard DNA copy numbers. Based on the results in hand, it is possible that (1) chytrid is not present in the ponds at New Afton mine, (2) chytrid is present but is not affecting the spadefoots, (3) the sensitivity of the SYBR Green assay was not sufficient to detect chytrid DNA, (4) PCR inhibitors interfered with the detection of chytrid DNA on samples, and (5) chytrid DNA did not adhere to the swabs that were used in this work. Future research should employ swabs with smaller tips and employ the more sensitive Taqman assay using a probe with a non-flourescent quencher (NFQ) as opposed to a black-hole quencher (BHQ-1) that was used here.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.070 | 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 teacher head, 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".