Pioneering contribution of Professor Bruce Ames to early development in biochemical aspects of oxidatively generated damage to DNA
Bibliographic record
Abstract
The first part of the memorial review article is devoted to a retrospective of selected topics that were the subject of pioneering studies over the period 1985-2025 by Professor Bruce Ames. Major efforts were made to develop accurate and sensitive assays including HPLC coupled with electrochemical detection for monitoring the formation of 8-oxo-7,8-dihydroguanine in isolated cells and animal tissues. Special attention was provided to the minimization of artefactual oxidation of DNA that occurs during sample preparation. Complementary information on the biological relevance of 8-oxo-7,8-dihydroguanine and 5,6-dihydroxy-5,6-dihydrothymine was gained from the non-invasive measurement of the oxidized bases and nucleosides in various mammalian fluids. The second part of this review focuses on the current situation concerning the formation of oxidized bases in cellular DNA produced under various conditions of oxidative stress and enzymatic ten-eleven TET-oxidation of 5-methylcytosine. The analysis of DNA base modifications by LC-MS/MS is the gold standard for the quantitative monitoring of base oxidation products in both DNA and several body fluids; oxidizing conditions that may not be suitable for biological studies. Low levels of oxidatively-induced lesions in cells are difficult to assess by chromatographic and MS methods because of a significant increase in the yields of oxidized bases/nucleosides above the background level including a significant contribution of adventitious oxidation reactions that cannot be totally suppressed. In a complementary way, the application of modified versions of the comet assay and alkaline elution techniques that target general classes of DNA lesions provides a more global account of damage although it gives less structural information about DNA damage formed under chronic exposure to mild oxidizing conditions.
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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 | 0.005 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.002 | 0.004 |
| Open science | 0.001 | 0.003 |
| Research integrity | 0.003 | 0.008 |
| Insufficient payload (model declined to judge) | 0.004 | 0.004 |
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".