Innate antiviral-like immune responses differ among divergent European and North \nAmerican farmed and wild Atlantic salmon (Salmo salar) and their hybrids
Bibliographic record
Abstract
This thesis involved a study of the effect of North American (NA) farmed, European \norigin (EO) farmed, wild, and related hybrid cross types on the innate antiviral-like immune \nresponse in Atlantic salmon (Salmo salar). Since the 1970s, millions of farmed salmon have \nescaped causing concern about how interbreeding with wild salmon may affect wild populations. \nFarmed and wild salmon differ genetically, yet the immune responses of farmed-wild hybrids are \nnot well understood. In Newfoundland, permission has been granted to start farming an EO \nstrain in addition to the current NA strain from the Saint John River. As these strains differ \ngenetically and geographically, there is concern about potential differences in immune responses. \nHence, I used real-time quantitative polymerase chain reaction (qPCR) with head kidney \ntemplates to measure expression of seventeen antiviral and other immune-relevant biomarker \ngenes (i.e., dhx58, gig1a, helz2, ifna, ifng, irf1a, irf7b, isg15a, mxb, pgds, rsad2a, rsad2b, stat1a, \nstat1c, tlr3, tlr7, and 5loxb) to assess the innate antiviral-like immune responses [i.e. to \nintraperitoneal (IP) injection with polyriboinosinic polyribocytidylic (pIC)] of six different \nAtlantic salmon cross types including pure crosses (i.e. NA, EO, and local Northeast Placentia \nRiver Wild) and three related hybrid crosses. Cross type abbreviations are as follows: pure Wild; \npure European farmed (Farm.EO); pure North American farmed (Farm.NA); wild female crossed \nwith Farm.EO male (Hyb.EO w♀); Farm.EO female crossed with wild male (Hyb.EO F♀); and \nFarm.NA female crossed with wild male (Hyb.NA F♀). At a basal transcript expression level, \nonly one gene (pgds) showed significant cross type differences, where Hyb.NA F♀ had \nsignificantly higher expression than the Wild and Hyb.EO F♀. After pIC injection, fifteen of the \nseventeen target genes (i.e. all except pgds and 5loxb) were significantly upregulated. In \naddition, there were significant cross type differences in transcript expression of ifna, isg15a, rsad2a, and rsad2b 24 hours post-injection, but only for pIC-injected fish and not the control fish \n(i.e., sterile phosphate buffered saline injected). The transcript expression of ifna was \nsignificantly higher in Farm.EO compared to Wild, Hyb.EO F♀, and Hyb.NAF♀, and also higher \nin Farm.NA than Wild. The transcript expression of both isg15a and rsad2a was significantly \nhigher in Farm.EO and Hyb.EO W♀ than Wild and Hyb.NA F♀. Lastly, the transcript expression \nof rsad2b was significantly higher in Hyb.EO W♀ than Wild. This experiment identified important \ndifferences in innate antiviral-like response among wild, farmed and related hybrid Atlantic \nsalmon. The results from this study support the hypothesis that interbreeding of wild and escaped \nfarm salmon may modulate the innate immune responses of the hybrid progeny compared with \nthe wild parents. They also suggest that hybridization may not negatively impact the innate \nimmune response in Atlantic salmon and therefore interbreeding resulting from escape events \nmay not pose a threat to the innate immune response of wild populations.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".