Comparative study of six methods of protein extraction for two-dimensional gel electrophoresis of proteomic profiling in poplar stems
Bibliographic record
Abstract
Azri, W., Ennajah, A. and Jing, M. 2013. Comparative study of six methods of protein extraction for two-dimensional gel electrophoresis of proteomic profiling in poplar stems. Can. J. Plant Sci. 93: 895–901. Protein extraction is a crucial step in two-dimensional gel electrophoresis (2-DE) analysis of proteins, since it can have significant impact on both the quantity and the quality of protein detection. The present study is a comparison between six previously published protocols of protein extraction (A, B, C, D, E, and F) aiming to determine a suitable method to extract total proteins from poplar stems, a recalcitrant plant tissue. The obtained results revealed that method F (optimized method B), combining detergents (CHAPS, Triton X-100, and low sodium dodecyl sulfate amounts) and chaotropes (thiourea and urea), gave the best solution for the problem of protein solubilization. Method F enabled the detection of more than 300 spots reproducible on the 2-DE gel with pH 4–7 immobilized pH gradient strips and 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis, using silver staining. Our results suggest that Method F is expected to have excellent applications in proteomic studies of poplar stems.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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 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".