Identification and characterization of novel genes involved in DNA double strand break repair process in the yeast Saccharomyces cerevisiae
Bibliographic record
Abstract
DNA Double Strand Break (DSB) is the most severe form of DNA lesion.Unrepaired DSBs and/or mutations in key DSB repair genes can lead to genomic instability, cancer or even cell death.DSBs can be repaired by two independent pathways; Homologous Recombination (HR) and Non-Homologous End Joining (NHEJ).Both pathways are highly conserved from yeast to human.HR requires a homologous region to repair the damage but in NHEJ, the break ends are ligated directly.In Saccharomyces cerevisiae, the key protein complexes of the NHEJ pathway are: Yku70p/Yku80p (YKU), which binds to DNA and initiates the process and stabilizes the broken ends, Mre11p/Rad50p/Xrs2p (MRX), which brings broken ends close together and Dnl4p/Lif1p/Nej1p, which have ligase activities.In this thesis, we aimed to identify novel proteins that influence the NHEJ process in yeast.To this end we performed a combination of high-throughput as well as lowthroughput assays, and followed-up by verifying some of the findings.The initial largescale plasmid repair screening that we performed revealed approximately 60 novel genes that might involve in the NHEJ process.Among these genes, PPH3/PSY2, HUR1, To my incredible supervisor, Dr. Ashkan Golshani, thank you for giving me the opportunity to work in your laboratory.Thank you for your support and guidance and mentorship.But mostly thanks for being such a great and understanding person.
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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 | 0.001 | 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".