Journal: International Journal of Molecular Sciences

Article Title: Regulation of Phenolic Compound Production by Light Varying in Spectral Quality and Total Irradiance

doi: 10.3390/ijms23126533

Figure Lengend Snippet: Heatmaps depicting similarities of PheC profiles among light treatments ( A ) as well as similarities in response of individual PheCs to the same light conditions ( B ). The relative contents of each PheC per treatment were averaged ( n = 5–6) and subsequently normalized to the maximum value among all light treatments. Cluster analysis was performed on normalized PheC quantitative data (distance function: Euclidean distance; linkage function: Average linkage). Specifications of light treatments: W (white), B (blue), R (red), G (green), L (low irradiance 100 µmol m −2 s −1 ), M (medium irradiance 200 µmol m −2 s −1 ), and H (high irradiance 400 µmol m −2 s −1 ). Compounds of interest: FQA (feruloylquinic acid), LUT (lutonarin), SAP (saponarin), ISD (isoscoparin derivative), HSG (homoorientin-7-O-[6-sinp]-glc), HFG (homoorientin-7-O-[6-fer]-glc), ISG (isovitexin-7-O-[6-sinp]-glc), and IFG (isovitexin-7-O-[6-fer]-glc).

Article Snippet: Further cluster analysis and heatmaps illustrating the differences in the relative content of PheCs across treatments differing in spectral compositions and irradiance were created (RStudio, ).

Techniques:

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