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  1. SciScore for 10.1101/2022.05.05.490805: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Informed consent for the use of human tissues was obtained from all subjects and approval was granted by the Institutional Review Board (IRB) of the University of Hong Kong and the Hospital Authority (Hong Kong West) (IRB approval no: UW 20-862).
    IRB: Informed consent for the use of human tissues was obtained from all subjects and approval was granted by the Institutional Review Board (IRB) of the University of Hong Kong and the Hospital Authority (Hong Kong West) (IRB approval no: UW 20-862).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationContamination: All cell lines were tested for mycoplasma every three months using the Lookout Mycoplasma PCR detection kit (Sigma-Aldrich) and were authenticated by ATCC®.

    Table 2: Resources

    Antibodies
    SentencesResources
    A Goat anti-hACE2 polyclonal primary antibody (at 1:100 dilution corresponding to a concentration of 2 µg/ml; Bio-techne, catalogue number #AF933) and an Alexa Fluor 488-conjugated donkey anti-goat secondary antibody (1:10,000 dilution, Jackson Laboratory, Catalog number # 305-547-003) were used for Western-blotting.
    anti-hACE2
    suggested: None
    anti-goat
    suggested: (Jackson ImmunoResearch Labs Cat# 305-547-003, RRID:AB_2339544)
    Experimental Models: Cell Lines
    SentencesResources
    Cell lines: Human primary embryonic kidney 293T/17 (HEK293T/17) cells, monkey kidney Vero E6 cells (Vero-E6), and Baby hamster kidney fibroblast 21 (BHK-21) cells were obtained from the American Type Culture Collection (ATCC® CRL-11268, ATCC® CRL-1586™, ATCC®
    Vero E6
    suggested: None
    HEK293T/17 cells were also used to produce MLV control and hACE2 nanoparticles.
    HEK293T/17
    suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
    In brief, HEK-293T/17 cells were co-transfected using Lipofectamine 2000 (Life Technologies) with MLV Gag-Pol packaging construct and the MLV transfer vector encoding a luciferase gene reporter either by itself (MLV-control) or with one of the Spike protein or hACE2 protein expression vectors for 48h at 37°C or 72h at 33°C.
    HEK-293T/17
    suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
    Infectious viral titers in culture supernatants were assayed by TCID50 in Vero-E6-TMPRSS2 cells.
    Vero-E6-TMPRSS2
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    The difference between parental BHK-21 cells in the presence and absence of wild-type pseudovirus was not significant (p-value: 0.37) and the difference between parental and hACE2-expresing BHK-21 cells in the presence of wild-type pseudovirus was highly significant (p-value: 1.57 e-13).
    BHK-21
    suggested: None
    Recombinant DNA
    SentencesResources
    Plasmids: The plasmids for MLV production, pCMV-MLV-gag-pol and pTG-Luc, were kindly provided by Jean Dubuisson (Institut Pasteur de Lille).
    pCMV-MLV-gag-pol
    suggested: None
    pTG-Luc
    suggested: None
    pcDNA3.1-SARS2-Spike1 and pcDNA3.1-hACE21 were obtained from Addgene (Addgene plasmids #145032; #145033); pCI-SARS2-Spike expressing a codon optimized version of the gene coding for S protein of SARS-CoV-2 was provided by Nicolas Escriou (Institut Pasteur).
    pcDNA3.1-SARS2-Spike1
    suggested: None
    pcDNA3.1-hACE21
    suggested: None
    pCI-SARS2-Spike
    suggested: None
    pUNO1-SpikeV8 carrying delta variant spike and pUNO1-SpikeV11 carrying omicron (B.1.1.529/BA.1 lineage) spike were purchased from InvivoGen (catalogue numbers p1-spike-v8 and p1-spike-v11 respectively).
    pUNO1-SpikeV11
    suggested: None
    Software and Algorithms
    SentencesResources
    All normalized data were then statistically analysed and represented using GraphPad Prism, version 9.3.1 (GraphPad Software).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Cryo-ET data collection of pseudovirus-infected cells: For pseudovirus-infected cells and lamellae, cryo-ET data were collected either using SerialEM on a Titan Krios G3i (Thermo Fisher Scientific) operated at 300kV, equipped with a K3 direct electron detector with a BioQuantum energy filter (Gatan Inc.) with energy slit set to 20 eV or a Glacios microscope (Thermo Fisher Scientific) operated at 200kV, equipped with a Falcon 3EC direct electron detector (Thermo Fisher Scientific).
    SerialEM
    suggested: (SerialEM, RRID:SCR_017293)
    Cryo-ET data processing: Automated real-time reconstruction protocols as implemented in the pyCoAn package, version 0.3 (github.com/pyCoAn/distro), an extended python version of the CoAn package13 were employed for all reconstructions.
    python
    suggested: (IPython, RRID:SCR_001658)
    CoAn
    suggested: None
    Segmentation of features of interest was achieved using manual tracing with Amira17, version 2019.4.
    Amira17
    suggested: None
    Tomogram slices were visualized with IMOD21, version 4.11.1, and segmentation results with Amira.
    Amira
    suggested: None

    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 did not find any issues relating to the usage of bar graphs.


    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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