Journal: PLoS Genetics

Article Title: A pals-25 gain-of-function allele triggers systemic resistance against natural pathogens of C . elegans

doi: 10.1371/journal.pgen.1010314

Figure Lengend Snippet: A) qRT-PCR of select ORR and IPR genes. * = Gene belongs to ORR and IPR, # = Gene belongs to only IPR, $ = Gene belongs to only ORR. The results shown are fold change in gene expression relative to WT. **** p < 0.0001, *** p < 0.001, ** p < 0.01, * p < 0.05, One-tailed t-test. n = 4 independent experimental replicates, different symbol shapes represent the expression values for replicates performed on different days. Bar heights indicate mean values and error bars represent standard deviations. B) Upregulated genes in both pals-25(Q293*) jy111 and pals-25(Q293*) icb98 mutants have significant overlap with genes regulated by wild-type pals-22 and pals-25 . Hypergeometric test, RF = 34.5; p < 5.39e-243 and RF = 15.6; p < 1.994e-182 for pals-25(Q293*) jy111 and pals-25(Q293*) icb98 , respectively. C-D) Upregulated genes in pals-25(Q293*) jy111 mutants have significant overlap with the IPR and ORR. Hypergeometric test, IPR: RF = 46.9; p < 6.215e-64, ORR: RF = 41.1; p < 6.883e-144. E-F) Upregulated genes in pals-25(Q293*) icb98 mutants have significant overlap with the IPR and ORR. Hypergeometric test, IPR: RF = 21.8; p < 4.529e-60, ORR: RF = 21; p < 5.122e-148. G) Correlation of differentially expressed genes in pals-25(Q293*) jy111 and pals-25(Q293*) icb98 mutants with those expressed during pathogen infection and regulated by known activators of the IPR. Correlation of gene sets quantified as Normalized Enrichment Score (NES) as defined by GSEAPreranked module analysis . Blue indicates significant correlation of downregulated genes in pals-25(Q293*) jy111 or pals-25(Q293*) icb98 mutants with the gene sets tested, and yellow indicates significant correlation of upregulated genes in pals-25(Q293*) jy111 or pals-25(Q293*) icb98 mutants with the gene sets tested. Grey indicates no significant correlation ( p > 0.05 or False Discovery Rate > 0.25). GSEA analysis of 93 gene sets tested can be found in . H) WormCat analysis shows significantly enriched gene categories represented in upregulated genes of pals-25(Q293*) jy111 and pals-25(Q293*) icb98 mutants. Bold text indicates broad “Category 1” biological processes enriched while nested text indicates more specific “Category 2 or 3” processes enriched. p values were determined using Fisher’s exact test with Bonferroni correction from minimum hypergeometric scores calculated in the WormCat software. A summary of WormCat analysis can be found in .

Article Snippet: A heatmap of the GSEA analysis was produced using Prism 9 (GraphPad).

Techniques: Quantitative RT-PCR, Gene Expression, One-tailed Test, Expressing, Infection, Software

Journal: ACS Chemical Neuroscience

Article Title: Interactions of Polychlorinated Biphenyls and Their Metabolites with the Brain and Liver Transcriptome of Female Mice

doi: 10.1021/acschemneuro.4c00367

Figure Lengend Snippet: PCB congener profile of the MARBLES mix differs from the profiles of the PCB tissue residues, as illustrated using (A) a stacked bar diagram and (B) a heatmap-like comparison of similarity coefficient cos θ between PCB congener profiles in different tissues and the MARBLES mix. PCB congener profiles are expressed as the mass percentage %. The tissue levels of the MARBLES PCB congeners and the corresponding OH-PCB metabolites depend on the dose and tissue. Heatmap-like illustrations of (C) PCB and (D) OH-PCB metabolite levels (ng/g, expressed on a log scale) from all exposure groups in the brain, liver, and serum typically show a dose-dependent increase in PCB and OH-PCB metabolite levels. Levels of representative PCB and OH-PCB congeners, including (E) PCB11, (F) PCB28, (G) PCB52, (H) 4–11, (I) 3′–28, and (J) 4–52. All values in the heatmap are log-transformed, and values in the bar graph are mean ± SD of the fresh-weight adjusted levels, with each value represented with an individual dot. Differences in PCB and OH-PCB levels by dose and tissue were assessed using 2-way ANOVA, followed by Tukey post hoc analysis, with p < 0.05 considered significantly different, and are summarized in Tables S2 and S3 . H, high dose; L, low dose; M, medium dose; ND, not detected.

Article Snippet: Heatmaps of PCB and OH-PCB metabolite levels were generated with log-transformed values by GraphPad Prism (RRID:SCR_002798) version 10.0.2.

Techniques: Comparison, Transformation Assay