<scp>HIV</scp> ‐1 establishes immediate latency in T cells expressing the viral Nef protein
Bibliographic record
Abstract
A variety of dual reporter HIV-1 derivatives have been developed that enable detection of infected cells independently from transcription initiated from the 5' LTR promoter. These reporters enable isolation of cells that are latently infected with HIV-1 provirus. We have previously described several dual reporter derivatives, including Red Green HIV-1 (RGH), which expresses mCherry from a constitutive internal promoter and GFP from the 5' LTR. A limitation of most dual HIV-1 reporter derivatives, including RGH, is that the Nef ORF is often disrupted to accommodate insertion of the internal reporter. Consequently, the potential role of Nef for establishment of latency using these reporters has not been clarified. To address this issue, we created three different RGH derivatives (RGHI), which express Nef from IRES elements downstream of the mCherry internal promoter. We found that each of these derivatives produced Nef protein at higher levels than wild-type LAI virus and that Nef expressed from each of the IRES elements was localized to the cell membrane. All of the Nef-expressing RGHI reporter viruses formed latent and productive infections and could be reactivated from latency at similar levels as the parental RGH derivative. These results indicate that expression of Nef does not affect the capability of HIV-1 to form latent infections. Furthermore, we propose that the RGHI derivatives described here represent novel tools to examine the role of Nef for HIV-1 replication.
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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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".