Transcriptome analysis of programmed cell death associated with allorecognition in chestnut blight fungus Cryphonectria parasitica
Bibliographic record
Abstract
In this thesis, I analysed transcriptional profiles of the chestnut blight fungus, Cryphonectria parasitica, during vegetative incompatibility (allorecognition) reactions due to differences at the vic3 locus.Out of a total 13944 identified expressed transcripts, including 2334 novel ones, only 1411 were differentially expressed during vic3 incompatibility reaction.Functional enrichment analysis showed increased expression of genes involved in detoxification and stress response (e.g.s Cytochrome p450, Glutathione S-transferase), and toxin biosynthesis.Surprisingly, even though the test strains were both the same mating type (MAT-2), genes involved in sexual reproduction (mf2-1, mf2-2 and mat-2) showed the most dramatic increase in expression during allorecognition response.Further qPCR analysis showed that activation of mating pheromone genes occurs during incompatible reactions involving five of the six known vic incompatibility loci.The only exception was vic4, which elicits a weak incompatibility and showed almost no change in pheromone gene expression.Analysis suggests that mf2-1, mf2-2 and mat-2 expression is triggered by activation of asexual sporulation.Genes encoded at the vic3 locus, vic3a and vic3b, were upregulated in barraging samples along with seven HET-domain genes located at other regions of the genome.Among the seven HET genes activated, one is located at the vic1 locus and previously implicated in vic1 incompatibility.Activation of these same HET domain genes also occurred in other vic incompatible pairings.For example, upregulation of dev3a and vic1a genes occurred during incompatibility reactions associated with each of the six known vic loci.This suggests that some HET genes serve as universal allorecognition factors.Furthermore, this data indicates that each incompatibility locus uses a set of several HET genes to iii activate Programmed Cell Death (PCD).In addition, I analysed the effects on barrage formation of p29, a protein-coding region from Cryphonectria hypovirus 1 (CHV1).Expression of p29 in C. parasitica was previously shown to delay the onset of vic3associated PCD.Results of the analysis indicated that ectopically expressed p29 does not have a strong modifying effect on gene expression in barraging strains.This study illustrates that nonself recognition is an active defence mechanism, where stress response and detoxification are combined with mycotoxins production.last 6 years couldn't have happened.You taught me how to do research and showed me what it means to be a good person.For six years working in Myron's team I was surrounded by wonderful colleagues.
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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 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 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".