Journal: medRxiv

Article Title: Polymorphism in IFNAR contributes to glucocorticoid response and outcome in ARDS and COVID-19

doi: 10.1101/2022.03.10.22272123

Figure Lengend Snippet: (A ) STAT1 expression in the lung after 4-day culture in the presence of IFN beta with or without hydrocortisone (HC). ( B) pSTAT1 expression in the same specimens as in A. ( C) Example photomicrographs showing higher STAT2 expression in a TT patient than in a CT patient and the effect of HC on its nuclear translocation. Most STAT2 remains in the cytoplasm of the CT patients, whereas nuclear expression is prominent in the TT patient. Indicated insets are shown in the bottom row. Arrows. ( D ) Combined results of all patients noting that two CT samples are excluded in the data as the patients were already under glucocorticoid treatment at the time of sample acquisition. Ns, not significant; *P<0.05; **P<0.01; and ***P<0.001

Article Snippet: The first stage antibodies were anti-alpha chain of the IFN alpha/beta receptor (St John’s Laboratory STJ112765) that was used 1:2000 and 1:5000 and anti-Stat1 (1:400, 9175S), anti-pStat1(1:100, 9167S) and anti-Stat2 (1:200, 72604S) all from Cell Signalling.

Techniques: Expressing, Translocation Assay

Journal: Scientific Reports

Article Title: Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes

doi: 10.1038/s41598-020-77289-3

Figure Lengend Snippet: Common microbial ecology indices of the upper airway microbiome in children with paired samples based on 16S ribosomal RNA sequencing and according to sample type. ( A ) Grouped bar graphs of selected indices showing no differences in community richness between nasal filters and nasal washes at the amplicon sequence variant unit (ASV) level. ( B ) Box-and-whisker plots of selected indices showing no differences in community α-diversity between nasal filters than in nasal washes at the ASV level. ( C ) Principal coordinates analysis (PCoA) plot of Bray–Curtis dissimilarities showing no distinct clustering by sample type at the ASV level. The lines connect samples with their group centroids. ( A , B ) were generated with the R package ggplot2 version 3.0.0 ( https://cran.r-project.org/web/packages/ggplot2/index.html) ; ( C ) was generated in vegan version 2.5-2 ( https://cran.r-project.org/web/packages/vegan/index.html ) and minor aesthetic edits were performed with Inkscape version 1.0.

Article Snippet: First, eukaryotic DNA was depleted using the NEBNext Microbiome Enrichment Kit (New England Biolabs).

Techniques: RNA Sequencing Assay, Amplification, Sequencing, Variant Assay, Whisker Assay, Generated

Journal: Scientific Reports

Article Title: Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes

doi: 10.1038/s41598-020-77289-3

Figure Lengend Snippet: Common microbial ecology indices of the upper airway microbiome in adults with paired samples based on 16S ribosomal RNA sequencing and according to sample type. ( A ) Grouped bar graphs of selected indices showing higher community richness in nasal filters than in nasal washes at the amplicon sequence variant (ASV) level. ( B ) Box-and-whisker plots of selected indices showing higher community α-diversity in nasal filters than in nasal washes at the ASV level. ( C ) Principal coordinates analysis (PCoA) plot of Bray–Curtis dissimilarities showing distinct clustering by sample type at the ASV level. The lines connect samples with their group centroids. ( A , B ) were generated with the R package ggplot2 version 3.0.0 ( https://cran.r-project.org/web/packages/ggplot2/index.html ) ; ( C ) was generated in vegan version 2.5–2 ( https://cran.r-project.org/web/packages/vegan/index.html ) and minor aesthetic edits were performed with Inkscape.

Article Snippet: First, eukaryotic DNA was depleted using the NEBNext Microbiome Enrichment Kit (New England Biolabs).

Techniques: RNA Sequencing Assay, Amplification, Sequencing, Variant Assay, Whisker Assay, Generated

Journal:

Article Title: Egr-1 Regulates Expression of the Glial Scar Component Phosphacan in Astrocytes after Experimental Stroke

doi: 10.2353/ajpath.2008.070648

Figure Lengend Snippet: Egr-1 binds to the phosphacan promoter in vivo. A: HeLa cells were transiently transfected with Egr-1 full-length human cDNA and subjected to ChIP with anti-Egr-1 antibody or rabbit IgG isotype control. Specific primers were used to amplify the area containing the putative Egr-1 site (lanes 1), or a distal, 4.5-kb upstream fragment (lanes 2). Genomic DNA input shows that the primers amplify bands of the expected size. Immunoprecipitation of sheared chromatin (ChIP) with anti-Egr-1 (α-Egr-1) produces a band of stronger intensity as compared with the distal site product and to control isotype IgG. B: HeLa cells were stimulated for 2 hours with PMA and ionomycin to induce endogenous Egr-1 and subjected to ChIP with anti-Egr-1 antibody or rabbit IgG isotype control. Precipitated DNA fragments were amplified with the same primers as in A surrounding the Egr-1 site (lanes 1) or the distal area (lanes 2). Genomic DNA input shows that primers amplify bands of the expected size. Immunoprecipitation of sheared chromatin (ChIP) with anti-Egr-1 (α-Egr-1) produces a band of stronger intensity as compared with the distal site product and to control isotype IgG. C: Immunoprecipitated DNA from the analysis in B was amplified and quantified by real-time PCR using primers surrounding the Egr-1 binding site or the distal area. Fold differences in the amounts of PCR products obtained with anti-Egr-1 antibody relative to isotype controls were calculated as described in Materials and Methods. Average values with SEM from five independent experiments are depicted. There is ∼6- to 10-fold higher amplification of the Egr-1 site fragment compared with the control fragment from the distal area.

Article Snippet: The three fragments were amplified using human genomic DNA as template (prepared with the Wizard genomic DNA purification kit, Promega) and inserted into the pGL3 promoter vector (Promega).

Techniques: In Vivo, Transfection, Control, Immunoprecipitation, Amplification, Real-time Polymerase Chain Reaction, Binding Assay