Additional file 1 of A unique effector secreted by Pseudozyma flocculosa mediates its biocontrol activity
Bibliographic record
Abstract
Additional file 1: Fig. S1. In vitro digestion of Pf2826 from Pseudozyma flocculosa using the ribonucleoprotein complex. A. Diagram of crRNA-173 binding site in the coding region of Pf2826. sign indicates the orientation of target strand. B. Agarose gels after electrophoresis show in vitro digestion at 37 °C for 2 hours of Pf2826 amplicons with or without sgRNA complexed with Cas9 protein. Fig. S2. Detection of successful CRISPR-Cas9 transformants using HRM analysis. Region surrounding the sgRNAbinding site were amplified from Cas9 transformants and wild type Pseudozyma flocculosa. Amplicons were subjected to high resolution melting curve analysis and difference curves displaying the difference in fluorescence were generated using Mic-qPCR software. The experiment is based on two technical replicates and repeated twice with similar results. Fig. S3. Confirmation of gene editing event. Coding sequence of Pf2826 was amplified from wild type Pseudozyma flocculosa and two positive transformants selected based on HRM analysis were sequenced. A. Pairwise chromatogram alignment of wild type, Pf2826AX and Pf282659X strains showing a single base deletion upstream to the PAM sequence in the mutant Pf2826AX. In the mutant Pf282659X, 59 bases were deleted around the sgRNA binding site. B. Pairwise protein sequence alignment of Pf2826 in wild type and mutant strains. Frame shift mutation caused by the single base deletion and 59 bases deletion has resulted in premature termination of translation. Fig. S4. Functional analysis of 79 candidate proteins interacting with Pf2826 from Pseudozyma flocculosa. Gene Ontology term annotation analysis of 79 potential interactors of Pf2826 was performed using Blast2GO. The proteins were annotated for molecular functions, cellular components, and biological process. The distributions are shown in percentage.
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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 | 0.002 | 0.016 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.858 | 0.210 |
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".