Additional file 1 of Control of vein-forming, striped gene expression by auxin signaling
Bibliographic record
Abstract
Additional File 1: Figure S1. ATHB8-, SHR-, and MP-Promoter-Driven Expression. (A–F) First leaves 4 DAG. Confocal laser scanning microscopy. Dashed white line: leaf outline. Top right: genotype. Bottom left: reproducibility index (number of samples with the displayed features / number of analyzed samples). (C) Co-expression of ATHB8::nCFP and SHR::nYFP during second loop formation. (E,F) Look-up table — ramp in G — visualizes YFP expression levels; blue: autofluorescence. Scale bars: (A,B,D–F) 25 μm; (C) 10 μm. Figure S2. MP::MP:YFP and MP::MP Functionalities in Vein Network Formation. Dark-field illumination of cleared first leaves 14 DAG. Top right: genotype. Scale bars: 0.5 mm. Figure S3. ATHB8 Expression Domains and MP and RIBO Expression Levels. First leaves 4 DAG. Confocal laser scanning microscopy. Top right: reporter. Dashed green outline: second loop nuclei expressing ATHB8::nCFP (A,B) or ATHB8::nYFP (D,E). (B,E) Look-up table — ramp in C — visualizes expression levels. Scale bars (shown, for simplicity, only in A and D): 5 μm. Figure S4. ATHB8 Expression Domains and RIBO Expression Levels. (A–E) First leaves 4 DAG. (A) Schematic of 4-DAG leaf — imaged in B–E — illustrating onset of ATHB8 expression (red) — imaged in B — associated with second loop formation [16, 22, 44]. Increasingly darker gray: progressively older ATHB8 expression domains. (B–E) Confocal laser scanning microscopy. (B) ATHB8::nYFP expression. (C) RIBO::nCFP expression. (D) Autofluorescence. (E) Overlay of images in B–D; red: ATHB8::nYFP expression; green: RIBO::nCFP expression; blue: autofluorescence. (F) RIBO::nCFP expression levels (mean ± SE) in nuclei at positions -2, -1, +1, and +2 — as defined in legend to Fig. 2 — relative to RIBO::nCFP expression levels in nuclei at position 0 — as defined in legend to Fig. 2 — during second loop formation. Difference between RIBO::nCFP expression levels in nuclei at position -2 or -1 and RIBO::nCFP expression levels in nuclei at position 0 was significant at P < 0.001 (***) by One-Way ANOVA and Tukey’s Pairwise test. Sample population sizes: 27 leaves; position -2, 42 nuclei; position -1, 64 nuclei; position 0, 69 nuclei; position +1, 50 nuclei; position +2, 28 nuclei. Scale bars (shown, for simplicity, only in column 2): 5 μm. Figure S5. mp-11 and MP::MP Effects on MP Expression. MP transcript levels in mp-11 and MP::MP seedlings relative to MP transcript levels in WT (mean ± SE of three technical replicates for each of three biological replicates). Seedlings 4 DAG. RT-qPCR. Difference between mp-11 and WT, and between MP::MP and WT was significant at P < 0.001 (***) by F-test and t-test with Bonferroni correction. Figure S6. ATHB8 Expression Domains and Levels in iaa12-1 and MP::VP16:bdlΔI;iaa12-1. (A,B) First leaves 4 DAG. Confocal laser scanning microscopy. Dashed white line: leaf outline. ATHB8::nYFP expression (look-up table — ramp in C — visualizes expression levels). Top right: genotype. Bottom left: reproducibility index (number of samples with the displayed features / number of analyzed samples). Scale bars: (A,B) 25 μm. Figure S7. Summary and Interpretation. A three-gene incoherent type-I feedforward loop [77] activates ATHB8 expression in narrow preprocambial stripes and leads to vein formation. MP receives the auxin input and activates expression of intermediate-loop AUX/IAA genes, which in turn inhibit MP expression [60, 64]. MP and AUX/IAA genes jointly regulate expression of the stripe gene ATHB8, which converts the auxin input into vein formation output. Arrows indicate positive effects. Blunt-ended lines indicate negative effects.
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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 | 0.010 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 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) | 0.993 | 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".