{"id":1119959,"date":"2023-12-14T03:37:46","date_gmt":"2023-12-14T08:37:46","guid":{"rendered":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/uncategorized\/the-dna-glycosylase-neil2-is-protective-during-sars-cov-2-infection-nature-com\/"},"modified":"2023-12-14T03:37:46","modified_gmt":"2023-12-14T08:37:46","slug":"the-dna-glycosylase-neil2-is-protective-during-sars-cov-2-infection-nature-com","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/dna\/the-dna-glycosylase-neil2-is-protective-during-sars-cov-2-infection-nature-com\/","title":{"rendered":"The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection &#8211; Nature.com"},"content":{"rendered":"<p><p>Ethics statement    <\/p>\n<p>    Human Study: The lung specimens from the COVID-19 positive    human subjects were collected using autopsy (study was IRB    Exempt). All donations to this trial were obtained after    telephone consent followed by written email confirmation with    next of kin\/power of attorney per California state law (no    in-person visitation could be allowed into the COVID-19 ICU    during the pandemic). The detailed patient characteristics were    published elsewhere (PMID: 34127431). For normal lung tissues,    lung biopsies were obtained after surgical resection of lungs    by cardiothoracic surgeons as before [https:\/\/elifesciences.org\/articles\/66417].    Deidentified lung tissues obtained during surgical resection,    which were deemed excess by clinical pathologists, were    collected using an approved human research protocol (IRB no.    101590). Blood samples were obtained from UTMB Biorepository of    research subjects with a laboratory diagnosis of COVID-19 that    consented to participate in the Clinical Characterization    Protocol for Severe Emerging Infections (UNMC IRB no.    146-20-FB\/UTMB IRB no. 20-0066). The normal healthy subjects    blood cell pellets were obtained under UTMB IRB no. 14-0131 and    20-0097.  <\/p>\n<p>    Animal (Hamster) study: Lung samples from 8-week-old male    Syrian hamsters were generated from experiments conducted    exactly as in previously published studies (PMID: 32540903).    Animal studies were approved and performed in accordance with    Scripps Research IACUC Protocol no. 20-0003 and UTMB IACUC    Protocol no. 2005060.  <\/p>\n<p>    Publicly available COVID-19 gene expression databases were    downloaded from the National Center for Biotechnology    Information (NCBI) Gene Expression Omnibus website    (GEO)69,70,71. If the dataset    was not normalized, RMA (Robust Multichip    Average)72,73 was used for    microarrays and TPM (Transcripts Per    Millions)74,75 was used for    RNASeq data for normalization. We used log2    (TPM+1) to compute the final log-reduced expression values    for RNASeq data. Accession numbers for these crowd-sourced    datasets are provided in the figures and manuscript. Single    Cell RNASeq data from GSE145926    was downloaded from GEO in the HDF5 Feature Barcode Matrix    Format. The filtered barcode data matrix was processed using    Seurat v3 R package76. Pseudo bulk    analysis of GSE145926    dataset was performed by adding counts from the different cell    subtypes and normalized using log2 (CPM+1). All of    the above datasets were processed using the Hegemon data    analysis framework77,78,79.  <\/p>\n<p>    Time (duration in hospital) and status (whether the patient is    discharged from hospital) were derived from the hospital-free    days post 45-day follow-up from COVID-19 patients    (n=100, GSE157103).    All non-COVID-19 patients (n=26, GSE157103)    were excluded from the analysis. KaplanMeier (KM) analysis is    performed using lifelines python package version 0.14.6. All KM    analyses use the StepMiner threshold+0.5 noise margin    as the threshold to separate the patients into high and low    groups.  <\/p>\n<p>    COVID-19 samples were inactivated by storing in 10 % formalin    for 2 days and then were transferred to zinc-formalin solution    for another 3 days. The decontaminated tissues were transferred    to 70% ethanol and cassettes were prepared for tissue    sectioning. The slides containing hamster and human lung tissue    sections were de-paraffinized in xylene (Sigma-Aldrich, catalog    no. 534056) and rehydrated in graded alcohols to water. For    NEIL2 antigen retrieval, slides were immersed in Tris-EDTA    buffer (pH 9.0) and boiled for 10min at 100C inside a    pressure cooker. Endogenous peroxidase activity was blocked by    incubation with 3% H2O2 for 10min. To    block non-specific protein binding 2.5% goat serum (Vector    Laboratories, catalog no. MP-7401) was added. Tissues were then    incubated with rabbit anti-NEIL2 polyclonal antibody (in house    generated, 33) for 1.5h at room temperature in a humidified    chamber and then rinsed with TBS or PBS 3x, 5min each.    Sections were incubated with horse anti-rabbit IgG (Vector    Laboratories, catalog no. MP-7401) secondary antibodies for    30min at room temperature and then washed with TBS or PBS 3x,    5min each; incubated with 3,3-diaminobenzidine    tetrahydrochloride (DAB) (Thermo Scientific, catalog no.    34002), counterstained with hematoxylin (Sigma-Aldrich, catalog    no. MHS1) for 30s, dehydrated in graded alcohols, cleared in    xylene, and cover slipped. Epithelial and stromal components of    the lung tissue were identified by staining duplicate slides in    parallel with hematoxylin and eosin (Sigma-Aldrich, catalog no.    E4009) and visualizing by Leica DM1000 LED (Leica Microsystems,    Germany).  <\/p>\n<p>    IHC images were randomly sampled at different 300300 pixel    regions of interest (ROI). The ROIs were analyzed using IHC    Profiler80. IHC Profiler    uses a spectral deconvolution method of DAB\/hematoxylin color    spectra by using optimized optical density vectors of the color    deconvolution plugin for proper separation of the DAB color    spectra. The histogram of the DAB intensity was divided into 4    zones: high positive (060), positive (61120), low positive    (121180) and negative (181235). High positive, positive, and    low positive percentages were combined to compute the final    percentage positive for each ROI. The range of values for the    percent positive is compared among different experimental    groups.  <\/p>\n<p>    Lung specimens from COVID-19 positive human subjects were    collected using autopsy procedures at the University of    California San Diego (the study was IRB Exempt) following    guidelines from the Centers for Disease Control and Prevention    (CDC) and College of American Pathologists autopsy committee.    All donations to this trial were obtained after telephone    consent followed by written email confirmation with next of    kin\/power of attorney per California state law (no in-person    visitation could be allowed into the COVID-19 ICU during the    pandemic). (<a href=\"https:\/\/www.cdc.gov\/coronavirus\/2019-ncov\/hcp\/guidance-postmortem-specimens.html\" rel=\"nofollow\">https:\/\/www.cdc.gov\/coronavirus\/2019-ncov\/hcp\/guidance-postmortem-specimens.html<\/a>    and     <a href=\"https:\/\/documents.cap.org\/documents\/COVID-Autopsy-Statement-05may2020.pdf\" rel=\"nofollow\">https:\/\/documents.cap.org\/documents\/COVID-Autopsy-Statement-05may2020.pdf<\/a>).    Lung specimens were collected in 10 % Zinc-formalin and stored    for 72h before processing for histology as done    previously81,82.  <\/p>\n<p>    Blood cell pellets stored in TRIzol LS Reagent (Invitrogen,    catalog no. 10296010) were obtained from the UTMB Biorepository    for Severe Emerging Infections from research subjects with a    laboratory diagnosis of COVID-19 that consented to participate    in the Clinical Characterization Protocol for Severe Emerging    Infections (UNMC IRB no. 146-20-FB\/UTMB IRB no. 20-0066).    Samples were used from subjects categorized as having moderate    or severe COVID-19 based on the following criteria: moderate    disease if requiring oxygen via nasal cannula, severe disease    if requiring oxygen via non-invasive ventilation (e.g., CPAP,    BiPAP, High-Flow nasal cannula, venturi mask). The normal    healthy subjects blood cell pellets were obtained in TRIzol    LS Reagent under UTMB IRB # 14-0131 and 20-0097. Total RNA was    isolated as per manufacturers protocol and subjected to real    time reverse transcriptase-quantitative Polymerase Chain    Reaction.  <\/p>\n<p>    Total RNA extraction was performed from cells using TRIzol    Reagent (Invitrogen, catalog no. 15596026) or TRIzol LS    Reagent. Total RNA (up to 2g) was used to synthesize cDNA    with a PrimeScriptTM RT Kit with gDNA Eraser    (TaKaRa, catalog no. RR047A) and qPCR was carried out using TB    Green Premix Ex Taq II (Tli RNase H Plus; TaKaRa, catalog no.    RR820A) in Applied Biosystems 7500 Real-Time PCR Systems with    thermal cycling conditions of 94C for 5min, (94C for 10s,    and 60C for 1min) for 40 cycles, and 60C for 5min. The    target mRNA levels were normalized to that of GAPDH or    18S RNA. Primer sequences used in the assay are    listed in Supplementary Table1. In each case,    DNase-treated RNA samples without reverse transcriptase were    amplified to test genomic DNA contamination.  <\/p>\n<p>    Syrian golden hamsters (Hamster\/Golden Syrian Hamster\/Male\/8    weeks old\/Charles River\/Strain Code 049) experiments were    approved by the Scripps Research Institute Institutional Animal    Care and Use Committee\/Protocol 20-0003, and were carried out    in accordance with recommendations. Lung samples were collected    from 8-week-old Golden Syrian hamsters post SARS-CoV-2    infection conducted exactly as in a previously published    study38. Briefly, lungs    from hamsters challenged with SARS-CoV-2 (1106    PFU) were harvested on day 5 (peak weight loss) and NEIL2    protein and mRNA levels were analyzed by IHC and RT-qPCR,    respectively. Syrian golden hamsters (Male\/8 weeks old) were    infected with SARS-CoV2 as approved by the UTMB IACUC (protocol    no. 2005060) and nuclear extract was prepared from the    uninfected and infected hamster lungs at 10 days post infection    as described before33,39, and DNA was    extracted from the same samples for LA-qPCR.  <\/p>\n<p>    A549 cells stably expressing human angiotensin I converting    enzyme 2 (A549-ACE2)83 is maintained in    Eagles Minimum Essential Media (EMEM; Gibco, Cat # 11095080),    containing 10% fetal bovine serum (FBS), 100units\/ml    penicillin and 100g\/mL streptomycin. A549-ACE2 cells grown in    six-well plates at ~70% confluence were transduced with    recombinant proteins using Pierce Protein Transfection Reagent    according to manufacturers recommendations (Pierce, Thermo    Scientific, catalog no. 89850). In brief, Pierce reagent    (dissolved in 250L of methanol or chloroform) was evaporated    to remove traces of solvent and 2g of rNEIL1, or rNEIL2    protein was added in PBS, vortexed, incubated for 5min at room    temperature, then the mixture was supplemented with serum free    medium. Mixtures were added directly onto the cell monolayers,    incubated for 4h in a 5% CO2 containing incubator    at 37C and then one volume of 20% serum-containing medium was    added for overnight. Transfection efficiency varied between 68    and 75% as determined in parallel experiments by indirect    immunofluorescence assays using anti-NEIL2 or anti-NEIL1 (in    house generated84) antibodies.    Transduced A549\/ACE2 cells were infected with SARS-CoV-2 at MOI    11.87. After incubation for an hour with viral inoculum, cells    were washed three times with EMEM. Infected cells were    harvested at indicated time points in various lysis buffers,    depending on the downstream experiment. Supernatants from    infected cells were harvested at 24h post-infection for    measuring the infectious virus titers by the TCID50    assay using Vero E6 cells. Briefly, 50L supernatants from    infected cells were serially diluted (10-fold) in EMEM    supplemented with 2% FBS; 100L of serially diluted samples    were added to Vero E6 cells grown in 96-well plates and    cultivated at 37C for 3 days followed by observation under a    microscope for the status of virus-induced formation of    cytopathic effect (CPE) in individual wells. The titers were    expressed as log TCID50\/mL.  <\/p>\n<p>    Human bronchial epithelium cell line, BEAS-2B (ATCC CRL-9609)    stably expressing NEIL2-FLAG,human gastric adenocarcinoma    (AGS, ATCC CRL-1739) and human embryonic kidney cells    (HEK29385) were grown at    37C and 5% CO2 in DMEM\/F-12 (1:1) containing 10%    FBS, 100units\/ml penicillin and 100units\/ml streptomycin. For    all experiments, 5060% confluent cells were used. We routinely    tested cell lines for mycoplasma contaminations using the    PCR-based Venor GeM Mycoplasma Detection Kit (Sigma, catalog    no. MP0025). Control or stable BEAS-2B cells at ~70% confluency    were transiently transfected with vector expressing GFP with    (SARS-CoV2-5-UTR-eGFP construct, synthesized and cloned by    GenScript Inc.) or without (UTR-Less-eGFP construct) UTR    (100ng) using Lipofectamine TM 2000 (Invitrogen, catalog no.    11668027), according to the suppliers protocol. To monitor    transfection efficiency, a reporter gene construct (0.25g)    containing -galactosidase downstream to the SV40 promoter was    co-transfected. Cells were allowed to recover for 16h in media    with serum and then GFP florescence was measured using an ECHO    florescent microscope (ECHO Revolve-R4). Total RNA and DNA were    isolated for subsequent qPCR analysis.  <\/p>\n<p>    The proteins in the nuclear extracts (from Hamster lungs)\/whole    cell extracts A549-ACE2 cells were separated onto a Bio-Rad    420% gradient Bis-Tris gel, then electro-transferred on a    nitrocellulose (0.45m pore size; GE Healthcare) membrane    using 1X Bio-Rad transfer buffer. The membranes were blocked    with 5% w\/v skimmed milk in TBST buffer (1X Tris-Buffered    Saline, 0.1% Tween 20) and immunoblotted with appropriate    antibodies SARS-CoV-2 spike protein (S1-NTD) (Cell Signaling    Technology, catalog no. 56996S), GAPDH (BioBharati Life    Sciences, catalog no. AB0060), Histidine (BioBharati Life    Sciences, catalog no. AB0010), NEIL233, OGG1 (in-house    generated86), NEIL1 and APE1    (in-house generated87), and HDAC2    (Histone deacetylase 2, GeneTex, catalog no. GTX109642). The    membranes were extensively washed with 1% TBST followed by    incubation with anti-isotype secondary antibody (Cell Signaling    Technology, catalog no. 7074) conjugated with horseradish    peroxidase in 5% skimmed milk at room temperature.    Subsequently, the membranes were further washed three times    (10min each) in 1% TBST, developed and imaged using kwikquant    image analyzer and image analysis software (ver. 5.2) (Kindle    Biosciences). Due to cross reactivity of common secondary    antibody with the pre developed membrane, the samples were run    in parallel gels in similar conditions, and developed with    different antibodies. For all the primary antibodies, 1:1000    dilution was used and for secondary antibody, 1:2000 dilution    was used.  <\/p>\n<p>    RNA-ChIP assays were performed as described    earlier39. Briefly, cells    were cross-linked in 1% formaldehyde for 10min at room    temperature. Then 125mM Glycine was added for 5min at room    temperature to stop crosslinking and then samples were    centrifuged at 1000g at 4C for 5min to pellet the cells.    The cell pellet was re-suspended in sonication buffer,    containing 50mM Tris-HCl pH 8.0, 10mM EDTA and 1% SDS with 1X    Protease inhibitor cocktail and sonicated to an average DNA    size of ~300bp using a sonicator (Qsonica Sonicators). The    supernatants were diluted with 15mM Tris-HCl pH 8.0, 1.0mM    EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS containing    protease inhibitors, and incubated with anti-NEIL1, -NEIL2,    -FLAG (Millipore, catalog no. F1804) or normal IgG (Santa Cruz,    catalog no. sc-2025) antibodies overnight at 4C.    Immunocomplexes (ICs) were captured by Protein A\/G PLUS agarose    beads (Santa Cruz, catalog no. sc-2003), that were then washed    sequentially in buffer I (20mM Tris-HCl pH 8.0, 150mM NaCl,    1mM EDTA, 1% Triton-X-100 and 0.1% SDS); buffer II (same as    buffer I, except containing 500mM NaCl); buffer III (1% NP-40,    1% sodium deoxycholate, 10mM Tris-HCl pH 8.0, 1mM EDTA), and    finally with 1X Tris-EDTA (pH 8.0) buffer at 4C for 5min    each. RNase inhibitor (50Uml1, Roche, catalog no.    03335402001) was added to sonication and IP buffers, and    40Uml1 to each wash buffer. The ICs were    extracted from the beads with elution buffer (1% SDS and 100mM    NaHCO3) and de-crosslinked for 2h at 65C. RNA    isolation was carried out in acidic phenolchloroform followed    by ethanol precipitation with GlycoBlue (Life Technologies,    catalog no. AM9516) as a carrier. Reverse transcription and    cDNA preparation was performed using a PrimeScript RT Kit with    gDNA Eraser. RNA-ChIP samples were analyzed by qPCR using    specific primers (listed in Supplementary    Table1) and represented as    percentage input after normalization to IgG.  <\/p>\n<p>    Wild-type recombinant His-tagged -NEIL2, -NEIL2-ZnF mutant    (ZnF-NEIL2mut) and -NEIL1 proteins were purified from E.    coli using protocol as described earlier64. Briefly, pET22b    (Novagen) vector containing C-terminal 6xHis tagged Coding DNA    Sequence (CDS) of various proteins was transformed into E.    coli BL21(DE3) RIPL Codon-plus cells (Agilent technologies,    catalog no. 230280). The log-phase culture    (A600=0.40.6) of E. coli was induced with    0.5mM isopropyl-1-thio--D-galactopyranoside (IPTG) and grown    at 16C for 16h. After centrifugation, the cell pellets were    suspended in a lysis buffer (Buffer A) containing 25mM    Tris-HCl, pH 7.5, 500mM NaCl, 10% glycerol, 1mM    -mercaptoethanol (-ME), 0.25% Tween 20, 5mM imidazole, 2mM    phenylmethylsulfonyl fluoride (PMSF). After sonication, the    lysates were spun down at 13,000rpm and the supernatant was    loaded onto HisPur Cobalt Superflow Agarose (Thermo    Scientific, catalog no. 25228), previously equilibrated with    Buffer A, and incubated for 2h at 4C. After washing with    Buffer A with a gradient of increasing concentration of    imidazole (10, 20, 30, 40mM), the His-tagged proteins were    eluted with an imidazole gradient (80500mM imidazole in    buffer containing 25mM Tris-HCl, pH-7.5, 300mM NaCl, 10%    glycerol, 1mM -ME, 0.25% Tween 20). After elution, the peak    protein fractions (in the range of 100250mM imidazole) were    dialyzed against Buffer C (1X PBS, pH 7.5, 1mM dithiothreitol    (DTT), and 25% glycerol) and stored at 20C in aliquots.  <\/p>\n<p>    The Corona virus nsp12 (GenBank: MN908947) gene, cloned into a    modified pET24b vector, with the C-terminus possessing a 10     His-tag, was a gift from Dr. Whitney Yin. The plasmid was    transformed into E. coli BL21 (DE3) RIPL Codon-plus    cells, and the transformed cells were cultured at 37C in LB    media containing 100mg\/L ampicillin. After the    OD600 reached 0.8, the culture was cooled to 16C    and supplemented with 0.5mM IPTG. After overnight induction,    the cells were harvested through centrifugation, and the    pellets were re-suspended in lysis buffer (20mM Tris-HCl, pH    8.0, 150mM NaCl, 4mM MgCl2, 10% glycerol). The rest of the    procedure is same as above with following modifications: the    His-tagged protein was eluted with an imidazole gradient    (80250mM imidazole in buffer containing 20mM Tris-HCl, pH    8.0, 150mM NaCl, 4mM MgCl2, 10% glycerol).    Similarly, nsp7 and nsp8 genes, individually cloned in pET22b    and pET30a+ vectors, respectively, were expressed in E.    coli as described in case of NEIL proteins. After elution,    the peak protein fractions of these proteins were dialyzed    against Buffer D (20mM Tris-HCl, pH 8.0, 250mM NaCl, 1mM    DTT, 25% glycerol) and stored at 20C in aliquots.  <\/p>\n<p>    For assembling the stable nsp12-nsp7-nsp8 complex, purified    nsp12 was incubated with nsp7 and nsp8 at 4C for three hours,    at a molar ratio of 1: 2: 2 in a buffer containing 20mM    Tris-HCl, pH 7.5, 250mM NaCl and 4mM    MgCl288.  <\/p>\n<p>    RdRp assay for CoV-2-5-UTR ZnF-site was conducted using a    self-priming RNA oligo and one short RNA oligo was used as the    primer for such assay for CoV-2-3-UTR ZnF-site containing    sequence as template (Supplementary Table3). Oligos were mixed    at the following final concentrations in 20L reaction volume:    Tris-HCl (pH 8, 25mM), RNA short primer (200M), RNA template    (2M), [32P]-UTP (0.1M), BSA (1mg\/ml), 0.1M    GTP, CTP, ATP and 0.01M UTP and SARS-CoV-2 RdRp complex    (~0.1M) on ice. For NEIL2 binding, the indicated    concentrations of NEIL2 were incubated in the buffer with RNA    on ice for 15min. Reactions were stopped after 15, 30 or    60min by the addition of 20L of a formamide\/EDTA (50mM)    mixture and incubated at 95C for 10min. Samples were run in    a 8% urea PAGE using 1x Tris-borate-EDTA as the running buffer.    The gels were exposed to a Phosphor screen for 46h and images    analyzed using a Typhoon FLA 7000 phosphorimager (GE    Healthcare).  <\/p>\n<p>    RNA-EMSAs with full length CoV-2 5- and 3-UTRs were carried    out as previously described89 with some    modifications. Briefly, the 297-nt long 5- and the 200-nt long    3-UTR RNAs (sequences in Supplementary    Table2, synthesized and    cloned in plasmids by GenScript Inc.) were synthesized by in    vitro transcription and end-labeled with [-32P]    ATP. The indicated concentrations of components were mixed in    15l reactions containing 0.3% poly (vinyl alcohol) (Sigma,    catalog no. P-8136), 2mM MgCl2, 0.1 U RNase    inhibitor (Biobharati Life Science, India), 1mM DTT, 20mM    HEPES-NaOH pH 7.5, 150mM NaCl, and 20% glycerol, and incubated    at room temperature for 5min. The RNA-protein complexes were    resolved on a native gel (4% 89:1 polyacrylamide gel containing    2.5% glycerol, 50mM Tris, and 50mM glycine) at 4C for    90min. Our EMSAs were designed to examine both the affinity    (when RNA is in trace amount) and the stoichiometry (when RNA    is not in trace amount) of the protein component required to    form complexes following principles described    before90. Hill    coefficient was calculated as described    before89. RNA-EMSA with    short (38-mer) oligonucleotide (oligo) probes were performed as    described before36,91, with some    modifications. Sequences of the oligonucleotides are listed in    Supplementary Table3. Briefly,    [-32P]ATP labeled RNA oligos were incubated with    101000nM of purified protein in a binding buffer containing    10mM Tris-HCl buffer (pH 7.6), 15mM KCl, 5mM    MgCl2, 0.1mM DTT, 10 U of RNase inhibitor, 1g    BSA, and 0.2mg\/ml yeast tRNA in a 1020l reaction volume.    After a 10-min incubation at room temperature RNA-protein    complexes were resolved on a 5% non-denaturing polyacrylamide    gel at 120V using 0.5x Tris-borate-EDTA as the running buffer    at 4C. For titration assays with short oligos the reaction    mix was prepared without yeast tRNA. Gels were fixed in an    Acetone: Methanol: H2O (10:50:40) solution for    10min, exposed to a Phosphor screen for 1216h and scanned    using Typhoon FLA 7000 phosphorimager.  <\/p>\n<p>    Lung tissues from freshly euthanized uninfected and SARS-CoV-2    infected hamsters were used for DNA damage analysis. Genomic    DNA was extracted using the Genomic tip 20\/G kit (Qiagen) per    the manufacturers protocol, to ensure minimal DNA oxidation    during the isolation steps. The DNA was quantitated by Pico    Green (Molecular Probes) in a black-bottomed 96-well plate and    gene-specific LA-qPCR assays were performed as described    earlier33,39 using LongAmp    Taq DNA Polymerase (New England Biolabs, Catalog no. M0323).    The LA-qPCR reaction was set for all genes from the same stock    of diluted genomic DNA sample, to avoid variations in PCR    amplification during sample preparation. Preliminary    optimization of the assays was performed to ensure the    linearity of PCR amplification with respect to the number of    cycles and DNA concentration (1015ng). The final PCR reaction    conditions were optimized at 94C for 30s; (94C for 30s,    5560C for 30s depending on the oligo annealing temperature,    65C for 10min) for 25 cycles; 65C for 10min. Since    amplification of a small region is independent of DNA damage, a    small DNA fragment (~200500bp) from the corresponding gene(s)    was also amplified for normalization of amplification of the    large fragment. Primer sequences used in the assay are listed    in Supplementary Table1. The amplified    products were then visualized on gels and quantitated with    ImageJ software (NIH). The extent of damage was calculated in    terms of relative band intensity with the uninfected control    mice\/hamster sample considered as 100.  <\/p>\n<p>    All statistical tests were performed using R version 3.2.3    (2015-12-10). Standard t-tests were performed using python    scipy.stats.ttest_ind package (version 0.19.0) with Welchs Two    Sample t-test (unpaired, unequal variance (equal_var=False),    and unequal sample size) parameters. Multiple hypothesis    correction was performed by adjusting p values with    statsmodels.stats.multitest.multipletests (fdr_bh:    Benjamini\/Hochberg principles). The results were independently    validated with R statistical software (R version 3.6.1;    2019-07-05). Pathway analysis of gene lists were carried out    via the Reactome database and algorithm. Reactome identifies    signaling and metabolic molecules and organizes their relations    into biological pathways and processes. Kaplan-Meier analysis    was performed using lifelines python package version 0.14.6.    Violin and Swarm plots were created using python seaborn    package version 0.10.1.  <\/p>\n<p>    Graph generation and analysis of statistical significance    between two sets of data were performed with Microsoft excel,    GraphPad Software (<a href=\"https:\/\/www.graphpad.com\/quickcalcs\/pvalue1.cfm\" rel=\"nofollow\">https:\/\/www.graphpad.com\/quickcalcs\/pvalue1.cfm<\/a>)    and MedCalc statistical software (<a href=\"https:\/\/www.medcalc.org\/calc\/comparison_of_means.php\" rel=\"nofollow\">https:\/\/www.medcalc.org\/calc\/comparison_of_means.php<\/a>).    p=values<0.05 were considered statistically    significant.  <\/p>\n<p>    Further information on research design is available in    theNature Portfolio    Reporting Summary linked to this article.  <\/p>\n<p><!-- Auto Generated --><\/p>\n<p>The rest is here:<br \/>\n<a target=\"_blank\" href=\"https:\/\/www.nature.com\/articles\/s41467-023-43938-0\" title=\"The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection - Nature.com\" rel=\"noopener\">The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection - Nature.com<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p> Ethics statement Human Study: The lung specimens from the COVID-19 positive human subjects were collected using autopsy (study was IRB Exempt). All donations to this trial were obtained after telephone consent followed by written email confirmation with next of kin\/power of attorney per California state law (no in-person visitation could be allowed into the COVID-19 ICU during the pandemic). The detailed patient characteristics were published elsewhere (PMID: 34127431).  <a href=\"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/dna\/the-dna-glycosylase-neil2-is-protective-during-sars-cov-2-infection-nature-com\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[26],"tags":[],"class_list":["post-1119959","post","type-post","status-publish","format-standard","hentry","category-dna"],"_links":{"self":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1119959"}],"collection":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/comments?post=1119959"}],"version-history":[{"count":0,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1119959\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/media?parent=1119959"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/categories?post=1119959"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/tags?post=1119959"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}