An FTIR study of <i>Pseudomonas aeruginosa</i> PAO1 biofilm development: interpretation of ATR–FTIR data in the 1500–1180 cm<sup>−1</sup> region
Bibliographic record
Abstract
Infrared spectra of Pseudomonas aeruginosa PAO1 biofilms grown on 40° ZnSe and 40° AMTIR (amorphous material transmitting infrared radiation, Ge33As12Se55) internal reflection elements (IRE) at 26 °C in a flow cell were collected. The depth of penetration of the evanescent wave was sufficient to identify four biofilm stages during the experiment: (1) cell/substratum attachment, (2) lag phase, (3) later-stage growth, and (4) restructuring (e.g. rearrangement, detachment or “erosion”). Our experimental results provide the first detection via a non-perturbative technique of an excess of protein in the neighbourhood of the surface. Our mathematical analysis applied to the data supports the conclusion that our observations cannot be completely accounted for by the changing characteristics of bacterial proteins but, rather, shows that an accumulation of excess protein near the attachment surface is taking place. On the assumption that biofilm cells are approximately of the same size as those of the planktonic culture, this suggests the presence of extracellular proteins. Our data do not support the presence of extracellular nucleic acids near the attachment surface in these biofilms. This conclusion is based on our observation that, during the initial 20 h of development (stage 2 and the beginning of stage 3), biofilms had a higher proportion of protein to nucleic acid than in the latter part of stage 3 and in stage 4. In the restructuring phase this ratio became equal to the ratio determined for planktonic cultures. The decrease of biomass during stage 4 is inconsistent with the physical removal or sloughing-off of cellular aggregates from biofilms within a few micrometres of the substrate surface but, instead, supports a model of gradual cell migration away from it. During this cell migration there is also a gradual loss of extracellular protein. Alternatively, therefore, the restructuring may involve cell lysis and the observed loss of biomass may be due to soluble macromolecules being removed from the neighbourhood of the surface.
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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 | 0.000 | 0.000 |
| 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) | 0.001 | 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".