Journal: International Journal of Molecular Sciences

Article Title: Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata , by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

doi: 10.3390/ijms18020317

Figure Lengend Snippet: Scatter plot analysis of hybridization success across 12 microarray experiments. To evaluate probe correction in the expression data for annotated target (three probes/target) we randomly selected two of the three probes present for each target (technical bias). For each gene, Pearson correlation coefficient was calculated within arrays. LPS, lipopolysaccharide; PGN, peptidoglycan.

Article Snippet: Primocin, LPS and PGN ( Escherichia coli O111:B4) were purchased from Invivogen (Nucliber, Spain).

Techniques: Hybridization, Microarray, Expressing

Journal: International Journal of Molecular Sciences

Article Title: Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata , by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

doi: 10.3390/ijms18020317

Figure Lengend Snippet: Venn diagram summarizing the quantitative variation of gene expression. The numbers inside the Venn diagrams indicate the number of mRNAs by treatment; number and percentage of mRNA probes with a fold change over 2 ( FC > 2) by treatment. The semicircular portion of the Venn diagram represents the overlaps between differentially expressed transcripts (FDR 5%) of both treatments PGN and LPS, which represent 53% and 84% of their transcriptomic response, respectively. White circle PGN, Black circle LPS.

Article Snippet: Primocin, LPS and PGN ( Escherichia coli O111:B4) were purchased from Invivogen (Nucliber, Spain).

Techniques: Expressing

Journal: International Journal of Molecular Sciences

Article Title: Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata , by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

doi: 10.3390/ijms18020317

Figure Lengend Snippet: ( a ) Common selected transcripts expressed in macrophages under LPS and PGN treatment; and ( b ) overexpressed GO categories ( p < 0.01) of the common macrophage transcripts expressed after treatments with PGN-LPS (No. Gene column shows the number of transcripts overexpressed in each GO category). FC, fold change.

Article Snippet: Primocin, LPS and PGN ( Escherichia coli O111:B4) were purchased from Invivogen (Nucliber, Spain).

Techniques: Binding Assay, Bacteria, Activation Assay

Journal: International Journal of Molecular Sciences

Article Title: Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata , by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

doi: 10.3390/ijms18020317

Figure Lengend Snippet: Heat map displaying hierarchical clustering results from microarray expression data common transcripts expressed after the challenge with LPS and PGN. Different genes are represented in different rows, and different experiments in different columns (PGN and LPS). Raw expression values are represented as a colour scale from green for lower expressions to red for higher expressions.

Article Snippet: Primocin, LPS and PGN ( Escherichia coli O111:B4) were purchased from Invivogen (Nucliber, Spain).

Techniques: Microarray, Expressing

Journal: International Journal of Molecular Sciences

Article Title: Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata , by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

doi: 10.3390/ijms18020317

Figure Lengend Snippet: Characterisation of the prostaglandin (PGE 2 ) response. PGE 2 levels in primary cell cultures stimulated for 1 and 6 h with PGN and 6 h with LPS (10 μg/mL) from Escherichia coli O111:B4. Results (mean ± SD; n = 6) from six independent experiments are expressed as pg of PGE 2 /mL.

Article Snippet: Primocin, LPS and PGN ( Escherichia coli O111:B4) were purchased from Invivogen (Nucliber, Spain).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata , by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

doi: 10.3390/ijms18020317

Figure Lengend Snippet: Quantitative RT-qPCR analysis of tumour necrosis factor-α (TNF-α) mRNA abundance in primary monocyte/macrophage-like cell cultures stimulated during 12 h with LPS, ultrapure LPS and PGN (10 µg/mL).

Article Snippet: Primocin, LPS and PGN ( Escherichia coli O111:B4) were purchased from Invivogen (Nucliber, Spain).

Techniques: Quantitative RT-PCR

Journal: Nature Microbiology

Article Title: Klebsiella oxytoca inhibits Salmonella infection through multiple microbiota-context-dependent mechanisms

doi: 10.1038/s41564-024-01710-0

Figure Lengend Snippet: ( a-c ) Heatmaps displaying growth displayed as area under curve in selected carbon sources for S . Tm in comparison with K. oxytoca MK01 WT and the sKO mutant after 24 h aerobic incubation using the Biolog microarrays PM1 and PM2a. Sugars are grouped based on their chemical structure with simple sugars and sugar alcohols displayed in ( a ), sugar acids, amines and ketones displayed in ( b ) and amino acids and nucleosides displayed in ( c ). Color scale bar shows AUC over the period of 24 h aerobic incubation. ( a-c ) Results represent mean (average growth) values of n = 3 independent measurements. ( d-g ) Growth curves of S . Tm and MK01 WT and sKO in selected carbon sources including ( d ) dulcitol, ( e ) raffinose, ( f ) sucrose and ( g ) tagatose. Results represent mean ± SEM growth values of n = 3 independent measurements with n = 2 technical replicates. ( h ) S . Tm CFUs and ( i ) K. oxytoca / E. coli CFUs in MM9 medium supplemented with 5 g/l or 10 g/l dulcitol after 24 h of co-cultivation in a 1:1 ratio. Results represent mean ± SEM of n = 2 independent experiments performed in n = 2 technical replicates.

Article Snippet: Extended Data Fig. 9 K. oxytoca and Salmonella have distinct but partially overlapping carbohydrate preferences and likely compete for various substrates. ( a-c ) Heatmaps displaying growth displayed as area under curve in selected carbon sources for S . Tm in comparison with K. oxytoca MK01 WT and the sKO mutant after 24 h aerobic incubation using the Biolog microarrays PM1 and PM2a.

Techniques: Comparison, Mutagenesis, Incubation