Involvement of Toxoplasma gondii natural antisense transcripts in cellular stress responses
Bibliographic record
Abstract
Natural antisense transcripts (NATs), as a major subset of long non-coding RNAs (lncRNAs), are derived from every chromosome of Toxoplasma gondii , with the highest occurrence from ChrIa (18.4 NATs per Mbp) and the lowest from ChrIX (3.9 NATs per Mbp). GO analysis indicates that genes, which mRNA-NAT pairs are derived, are important for house-keeping and essential activities of T. gondii . Approximately half of protein encoding genes, whose loci also generate NATs, are involved in biological processes of metabolic processes and protein biochemistry and have canonical catalytic or binding activities. Using NAT of ubiquitin-like protease 1 ( TgUlp1 -NAT) as our study model, we showed that TgUlp1 -NAT expression is part of cellular stress responses. Using a nanoluc reporter system, we confirmed that electroporation or membrane destabilization significantly induced TgUlp1 -NAT expression. When the extracellular parasites were exposed to media containing high potassium, high sodium or altered osmotic pressure, TgUlp1 -NAT expression was significantly down-regulated. In addition, two TgUlp1 -NAT variants were detected in stressed T. gondii . One is an intron-retained variant, and the other is a spliced variant, referred to as TgUlp1 -NATa and TgUlp1 -NATb, respectively. The intronic sequence is 368 nts long, where regulatory small ncRNAs were derived. Taken together, we have confirmed that NAT expressions and functions are involved in cellular adaptation that allows T. gondii recover from stresses. • Natural antisense transcripts are abundant in Toxoplasma gondii genome (∼ 12 per Mbp) • ∼50% of Toxoplasma natural antisense transcripts ( Tg NATs) have 3’-overlapping with mRNA • Membrane destabilization and the change in salinity and osmotic pressure significantly alter TgUlp1 -NAT expression • Under stresses, alternative splicing of TgUlp1 -NAT yields two transcript variants
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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".