Analysing photosynthetic complexes in uncharacterized species or mixed microalgal communities using global antibodies
Bibliographic record
Abstract
Photoautotrophs share core pathways for primary productivity and elemental cycling. These paths are generally mediated by abundant protein complexes which are conserved across wide taxonomic ranges, and which quantitatively dominate the proteomes of photoautotrophs. Quantification of key protein pools is a powerful approach to measure resource allocations and maximal catalytic capacities for biological functions, for comparing species or communities, or for tracking change over time within communities. Protein quantification can be more definitive than transcript analyses for functional studies, since changes in transcript levels are often only weakly coupled to pool sizes of functional protein. For field samples protein detections are more generally applicable than enzyme assays which require individually specialized extractions and assays, which are prone to interference by environmental contaminants. We are using bioinformatic analyses to design a series of peptide sequence tags that are conserved in all family members for a well‐characterized subunit from each of the major catalytic complexes mediating photosynthesis and nitrogen metabolism. We use these peptide sequence tags to elicit production of ‘global antibodies’, intended to recognize all members of the target protein family with equal efficiency regardless of the species of origin. Uniform target detection is particularly important for tracking levels of key proteins in mixed communities, or for quantitative comparisons across plant species. In parallel we are creating quantification standards for these key protein pools for functional and (eco)physiological studies.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 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) | 0.000 | 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 teacher head, 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".