Assessment of genotypic identity of cyanobacterial strains in culture collections using HIP1-based primers
Bibliographic record
Abstract
We examined 32 cyanobacterial strains, representative of 11 different genera, for the presence of the highly iterated genomic palindrome, called HIPI, using HIP I extended PCR primers. Cryolysates or cell suspensions, and even single colonies, of Microcystis aeruginosa, strain PCC 7806, yielded PCR products equivalent to those obtained with purified DNA, as judged from the banding patterns obtained by gel electrophoresis. Cryolysates were used for amplification and genotyping of all other strains. Representatives of different genera differed extensively in HIP1-based migration patterns, and the amplification products of axenic cyanobacteria were comparable to those obtained with duplicate, non-axenic strains. In addition, HIPI repeats were present in 11 strains of the species Microcystis aeruginosa and in isolates assignable to Planktothrix agardhii and P. rubescens. Based on available 16S rDNA sequence data and DNA/DNA hybridization results for members of these genera, the differences detected by HIP1-based profiling correlate with the interspecies distinctions between Planktothrix agardhii and P rubescens, and reflect intraspecific diversity for members of Microcystis aeruginosa. Thus, we have confirmed the value of this method for rapid genotyping and verification of presumably identical strains from different culture collections.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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".