Shrink it or lose it: balancing loss of function with shrinking genomes in the microsporidia
Bibliographic record
Abstract
Microsporidia are obligate intracellular parasites that have evolved an elaborate mechanism for invading animal host cells, but which have otherwise greatly reduced biological complexity. In particular, microsporidia possess the smallest autonomous nuclear genomes known (as opposed to nucleus derived organelles, or nucleomorphs), and their 'anaerobic' core carbon metabolism is severely limited. Here we compare the extremes to which these two characteristics have evolved, and contrast how their reduction has either proceeded within the constraints of an unchanging set of functions, or has reduced the functional capabilities of the cell. Specifically, we review how the smallest known nuclear genome, the 2.3 Mbp genome of Encephalitozoon intestinalis, has arrived at this diminutive form without significantly affecting its protein-coding complexity in comparison with closely related, larger genomes. In contrast to this, Enterocytozoon bieneusi has a relatively large genome, and yet has lost all enzymes necessary to synthesize ATP from sugar - imposing a major limitation on the functional capabilities of the cell. The extremity of this reduction demands a re-evaluation of metabolic processes in other microsporidia: although pathways such as glycolysis are present, comparative genomic data suggest they may not play the cellular role that they are generally assumed to play.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 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".