Journal: Frontiers in Immunology

Article Title: Integrated plasma metabolomic and cytokine analysis reveals a distinct immunometabolic signature in atopic dermatitis

doi: 10.3389/fimmu.2024.1354128

Figure Lengend Snippet: Non-targeted metabolomics profiling analysis of the plasma of atopic dermatitis (AD) patients and healthy controls (HC). For all scores plots, red=AD and green=HC. (A) PCA score plot with the first two components explaining for 80.1% of the variance. (B) PLS-DA score plot with the first two components explaining for 79.6% of the variance. (C) OPLS-DA score plot with the first two components explaining for 70% of the variance. (D) K-means clustering of groups. (E) Synchronized 3D scores and loading plots for visualization of the most influential compounds of the first three components on PCA. (F) Variable importance in projection (VIP) score ranking the most important metabolites.

Article Snippet: The heatmaps of data correlation between cytokines and metabolites were performed using Graphpad Prism 9.

Techniques: Clinical Proteomics

Journal: Frontiers in Immunology

Article Title: Integrated plasma metabolomic and cytokine analysis reveals a distinct immunometabolic signature in atopic dermatitis

doi: 10.3389/fimmu.2024.1354128

Figure Lengend Snippet: Metabolites with significant alterations in unmatched AD vs HC patients. (A) Volcano plot of significant fold change distribution of selected metabolites in AD versus HC (blue=significantly downregulated). (B) Boxplot summaries of the peak intensities of the significant metabolites (red=AD, green=HC). (C) Heatmap of the differential metabolites quantified in plasma in AD vs HC individuals using Euclidian distance measure and Ward clustering algorithm.

Article Snippet: The heatmaps of data correlation between cytokines and metabolites were performed using Graphpad Prism 9.

Techniques: Clinical Proteomics

Journal: Frontiers in Immunology

Article Title: Integrated plasma metabolomic and cytokine analysis reveals a distinct immunometabolic signature in atopic dermatitis

doi: 10.3389/fimmu.2024.1354128

Figure Lengend Snippet: Metabolites in atopic dermatitis patients with greater than two-fold change.

Article Snippet: The heatmaps of data correlation between cytokines and metabolites were performed using Graphpad Prism 9.

Techniques:

Journal: Nature Communications

Article Title: Natural variation of an E3 ubiquitin ligase encoding gene Chalk9 regulates grain chalkiness in rice

doi: 10.1038/s41467-025-61683-4

Figure Lengend Snippet: a The genome-wide association signals for chalky grain rate (CGR) and degree of chalkiness (DC) in the region at 18–21 Mb on chromosome 9 ( x -axis) across two years. Negative log 10 -transformed P values from the linear mixed model are plotted on the y -axis. The horizontal dashed line indicates the genome-wide significance threshold ( P = 1×10 –6 ). P values were determined using a two-sided Wald test and assessed after Bonferroni correction for multiple comparisons. b Linkage disequilibrium (LD) heatmap of the Chalk9 locus region. Pairwise linkage disequilibrium was determined by calculating r 2 (the square of the correlation coefficient between SNPs). c Relative expression level of the 12 candidate genes in the endosperm of eight high-chalky and eight low-chalky varieties at 20 days after flowering (DAF). The 12 predicted genes in the Chalk9 locus region are labeled by I to XII. Data show means ± SD ( n = 8 varieties). P values were calculated for comparisons between high-chalky and low-chalky groups, with each group comprising 8 varieties. d Relative expression level of the candidate gene III ( Chalk9 ) in the endosperm from the selected varieties at 20 DAF. The P value was calculated for the comparison between high-chalky and low-chalky groups, with each group comprising 8 varieties. Data show means ± SD ( n = 3 biological replicates). e Relative expression level of the 12 candidate genes in the leaves of eight high-chalky and eight low-chalky varieties. Data show means ± SD ( n = 8 varieties). In c – e , statistical analysis between high-chalky and low-chalky groups was performed by two-tailed Student’s t -test. Source data are provided as a Source Data file.

Article Snippet: Correlation analysis, heatmap plotting, and volcano plot analysis were performed using BMKCloud ( www.biocloud.net ).

Techniques: GWAS, Transformation Assay, Genome Wide, Expressing, Labeling, Comparison, Two Tailed Test