1. Dixie Goss

    Review 2: "Single-Molecule Dynamics of SARS-CoV-2 5ʹ Cap Recognition by Human eIF4F"

    This preprint uses a single molecular assay to demonstrate that SARS-CoV-2 5’ translation is sensitive to the small molecule rocaglamide. Reviewers deem the methodology reliable with only minor follow-up experiments.

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  2. Review 1: "Single-Molecule Dynamics of SARS-CoV-2 5ʹ Cap Recognition by Human eIF4F"

    This preprint uses a single molecular assay to demonstrate that SARS-CoV-2 5’ translation is sensitive to the small molecule rocaglamide. Reviewers deem the methodology reliable with only minor follow-up experiments.

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  4. SciScore for 10.1101/2021.05.26.445185: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power AnalysisMovies were acquired for 10 minutes at 10 frames per second, under illumination with a 532 nm laser at a power of 0.70 µW/µm2, to excite Cy3 fluorophores.
    Cell Line AuthenticationAuthentication: 5 Traces containing robust smFRET signals for eIF4E–RNA interaction were selected by visual inspection.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Luciferase assays: 100 nM CoV firefly luciferase fusion RNA was added to 12 µL of HeLa lysate reaction mix from an in vitro protein expression kit (Thermo Scientific, 88882), along with 0.5 µL of rocaglamide/RocA solution (Med Chem Express, Product No. HY-19356) or 4E2RCat solution (Med Chem Express, Product No. HY-100733) in varying concentrations as indicated in the Results and Discussion.
    HeLa
    suggested: None
    Recombinant DNA
    SentencesResources
    For preparation of the luciferase fusion construct, DNA fragments containing the class II T7 promoter Φ2.5, followed by the SARS-CoV-2 5’ untranslated region sequence, the coding sequence for firefly luciferase, and the SARS-CoV-2 5’ untranslated region sequence were assembled in a pUC57 vector.
    pUC57
    suggested: RRID:Addgene_40306)
    The sequence was inserted into pUC119 via SalI and EcoRI restriction sites incorportated during gBlock synthesis.
    pUC119
    suggested: RRID:Addgene_50010)
    Preparation of fluorescently labeled eIF4E and eIF4E(S209D): The pET-28a(+) vectors containing the sequences of eIF4E or eIF4E(S209D), each fused with an N-terminal Protein G tag, were designed similarly to Feokistova et. al., (2013).
    pET-28a(+ )
    suggested: None
    The pULTRA expression vector, containing inserts encoding tRNACUA and pAzF-tRNACUA-synthetase – a generous gift from Abhishek Chatterjee, Boston College – was co-transformed into an E. coli BL95ΔAΔfabR strain with the pET28a(+)-eIF4E plasmid, and transformants were selected on LB agar containing Kanamycin (50 µg/mL) and Spectinomycin (100 µg/mL).
    pULTRA
    suggested: RRID:Addgene_24129)
    pET28a(+)-eIF4E
    suggested: None
    Software and Algorithms
    SentencesResources
    The full-length human GAPDH transcript sequence, obtained from UCSC Genome Browser, was purchased as a gBlock from IDT.
    UCSC Genome Browser
    suggested: (UCSC Genome Browser, RRID:SCR_005780)
    48 Event timings identified from ebFRET analysis were converted to empirical cumulative probability distributions for the times between events, and the event durations, then fit with single- or double-exponential models to determine kon or koff, according to the equations:

    Fitting was carried out in MATLAB by non-linear least-squares regression using the Trust-Region algorithm.

    MATLAB
    suggested: (MATLAB, RRID:SCR_001622)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).


    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.


    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).


    Results from JetFighter: We did not find any issues relating to colormaps.


    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.


    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

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