Additional file 1 of Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata
Bibliographic record
Abstract
Additional file 1: Additional Material 1-Supplementary Figure 1. The ESCRT machinery is composed of five sub-complexes each functioning consecutively for recruitment of the downstream subcomplex. The process begins with the recruitment of ESCRT0 or its analogue TOM1-esc for recognition of tagged Ubiquitin on cargo, and endosomal membrane phospholipids such as phosphatidylinositol 3-phosphate (PtdIns [3]P) upon which the ESCRTI, composed of VPS23, VPS28, and VPS37, is recruited, with its only known role being ubiquitin recognition via its UIM domain [18]. The assembly of ESCRTI then leads to assembly of the heterotetrameric ESCRTII consisting of VPS36, VPS22, and two copies of VPS25 which also bind to PtdIns [3]P via the FYVE domains [18]. Finally, this leads to the recruitment of the ESCRTIII machinery, a heteropentameric complex consisting of SNF7-domain containing family proteins, VPS20, VPS32, VPS2, VPS24, and CHMP7 [18]. A filamentous VPS32 polypeptide capped by VPS2 and VPS24 (also belonging to the paralagous SNF7-domain containing family of proteins) induces ILV formation by constricting the neck of the budding vesicle, a process which is catalysed by the ESCRTIIIA VPS4, an AAA+ ATPase [18]. It is also hypothesized that ESCRTIIIA components such as VPS31 and VPS46 are required for stabilizing the sub-complexes during the budding processes while others are needed for recycling of the complexes back into the cytosol once the process is complete [18]. Figure adapted from Stenmark and Raiborg [18].
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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 | 0.015 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.839 | 0.185 |
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".