nasopharyngeal swabs  (Bruker Corporation)

Journal: Microbiology Spectrum

Article Title: Immune horses rapidly increase antileukoproteinase and lack type I interferon secretion during mucosal innate immune responses against equine herpesvirus type 1

doi: 10.1128/spectrum.01092-24

Figure Lengend Snippet: Sample variation by PCA. EHV-1 immune ( n = 4) and non-immune ( n = 4) horses were intranasally challenged with 1 × 10 7 PFU of EHV-1 Ab4. RNA was extracted from nasopharyngeal swab samples, pre-infection (pre) and at 24hpi, and sequenced. Raw read counts were variance stabilizing transformation transformed, then linearly transformed by PCA for two-dimensional scaling of sample-to-sample variation. ( A ) PCA plot graphed on PC1 and PC2. Immune horses are shown in green and non-immune horses are shown in black. Filled circles represent the pre-infection timepoint and unfilled points represent 24hpi. ( B ) Pathway analysis of PCA rotation, displaying gene ontology biological process (GO:BP) pathways for PC1 (individual variation) and PC2 (pre- to 24hpi changes in gene expression). Upregulated pathways are shown in blue and downregulated pathways in red. The significance of pathway enrichment based on PC1 or PC2 is described by P -values.

Article Snippet: For RNA extraction, nasopharyngeal swabs were reconstituted in 800 µL MagMAX Lysis/Binding Solution and 250 µL of the sample was utilized for RNA sequencing (Ambion Inc, Austin, TX, USA).

Techniques: Infection, Transformation Assay, Expressing

Journal: Microbiology Spectrum

Article Title: Immune horses rapidly increase antileukoproteinase and lack type I interferon secretion during mucosal innate immune responses against equine herpesvirus type 1

doi: 10.1128/spectrum.01092-24

Figure Lengend Snippet: Differential expression of genes in non-immune compared to immune horses during early infection with EHV-1. RNAseq was used to quantify nasopharyngeal gene expression in EHV-1 immune and non-immune horses, pre-infection and at 24hpi. DE genes were determined by DESeq2, and gProfiler was used to determine the immune relevance of DE genes. ( A ) Number of DE genes between immune and non-immune horses, pre-infection (bottom) and at 24hpi (top) with genes upregulated in immune horses to the left and genes upregulated in non-immune horses to the right. The fraction of DE genes related to the immune response is shown in black, and genes involved in other biological processes are in gray. Genes were selected with a P -adj <0.10. ( B ) Volcano plot of group-specific LogFC against P -adj, dotted lines are the cut-off values for significant differential expression of Log2FC > 1.5 and P -adj <0.05. Green points represent annotated genes upregulated in immune horses, and black dots represent annotated genes upregulated in non-immune horses. Larger points with gene labels represent the selected gene for each group. ( C ) Heatmap with relative gene expression of each significantly upregulated gene by row. Columns under the green bar represent immune horses and columns under the black bar represent non-immune horses. Genes in black rows are upregulated in non-immune horses and genes in green rows are upregulated in immune horses. The intensity of shading represents relative expression in Log2FC for each horse. Selected genes are shown in black font. *Marks genes involved in the immune response.

Article Snippet: For RNA extraction, nasopharyngeal swabs were reconstituted in 800 µL MagMAX Lysis/Binding Solution and 250 µL of the sample was utilized for RNA sequencing (Ambion Inc, Austin, TX, USA).

Techniques: Expressing, Infection

Journal: Microbiology Spectrum

Article Title: Immune horses rapidly increase antileukoproteinase and lack type I interferon secretion during mucosal innate immune responses against equine herpesvirus type 1

doi: 10.1128/spectrum.01092-24

Figure Lengend Snippet: Mucosal SLPI mRNA expression in response to EHV-1 infection resembles protein secretion kinetics in immune horses. SLPI mRNA expression and protein secretion were measured at the URT and at additional timepoints in EHV-1 infection. SLPI mRNA was measured by RNAseq in nasal cells and protein secretion was measured by bead-based assay in the soluble fractions from the same nasopharyngeal swab samples. Immune horses are shown in green and non-immune horses are shown in black. ( A and B) mRNA expression of SLPI compared to SLPI secretion in (A) immune horses and (B) non-immune horses. Solid lines indicate mRNA expression and dashed lines represent protein secretion. Graphs show the median and SEM.

Article Snippet: For RNA extraction, nasopharyngeal swabs were reconstituted in 800 µL MagMAX Lysis/Binding Solution and 250 µL of the sample was utilized for RNA sequencing (Ambion Inc, Austin, TX, USA).

Techniques: Expressing, Infection, Bead-based Assay

Journal: Trials

Article Title: Impact of oral azithromycin and intermittent preventive treatment with sulfadoxine-pyrimethamine regimen on child mortality in Sierra Leone: trial protocol for a randomised, two-arm, double-blinded, placebo-controlled clinical trial (ICARIA)

doi: 10.1186/s13063-024-08443-9

Figure Lengend Snippet: Participant timeline

Article Snippet: The first nasopharyngeal swab of the participant is immediately placed into 1 ml skim milk-tryptone-glucose-glycerol medium and the second nasopharyngeal specimen is stored in DNA/RNA Shield (Zymo Research) as a backup sample and, if required, to analyse the microbiome and resistome of the nasopharyngeal samples using a shot-gun approach [ ].

Techniques: