loganic acid  (MedChemExpress)

Journal: bioRxiv

Article Title: Single-cell metabolome and RNA-seq multiplexing on single plant cells

doi: 10.1101/2025.05.20.655036

Figure Lengend Snippet: UMAP showing clustering of cell types by gene expression and metabolite expression. A. Marker gene guided cell type annotation in RNA-UMAP plot. B. Targeted analyte guided cell type annotation in MET-UMAP plot. C. These two different UMAP plots were connected based on their corresponding well identities, where cells are colored with annotations based on representative metabolite accumulation (serpentine, secologanin, mauritianin, loganic acid). D. Sankey plot showing similarities and differences when cells are annotated with gene markers or metabolites. The height of the plot is proportional to the number of cells. The left side represents the marker gene-based cell type annotation, and right side represents metabolite-based annotation.

Article Snippet: Commercially available analytical standards used in this study included: loganic acid (Extrasynthese), secologanin (Sigma Aldrich), mauritianin (BIOMOL GmbH), ajmalicine (Sigma Aldrich), catharanthine (Abcam), deacetylvindoline (Toronto Research Chemicals Inc), anhydrovinblastine disulfate (Toronto Research Chemicals Inc.), vinblastine sulfate (Thermo Scientific Chemicals), serpentine hydrogen tartrate (from Sequoia Research Products Ltd.), ajmaline (Extrasynthese), tabersonine (TCI, Tokyo Chemical Industry Co. Ltd.), vindolinine (Advanced ChemBlocks Inc.), vindoline (Acros Organics).

Techniques: Gene Expression, Expressing, Marker

Journal: bioRxiv

Article Title: It runs in the family: Discovery of enzymes in the oleuropein pathway in Olive ( Olea europaea ) by comparative transcriptomics

doi: 10.1101/2025.03.20.644408

Figure Lengend Snippet: Schematic of differentially expressed genes (DEG) belonging to enriched KEGG modules of terpenoid biosynthesis, increasing (M00095 – MVA pathway; top) or decreasing (M00096 – MEP pathway; center) during olive maturation and ripening. The secoiridoid biosynthetic pathway is shown at the bottom, with enzymes characterized in this work shown in olive green; ligstroside biosynthesis remains unsolved and thus it is represented as disconnected. Heatmaps show expression patterns of all DEGs (one per row) annotated as the KEGG orthology number shown below each plot, with colors showing the average of the log-transformed transcripts per million (log 2 (TPM+1)) of all species, with color-scale ranging from the minimum (blue) to the maximum (red) mean expression value per gene (row.) Scatter plots show the mean (dots) and standard deviation (bars) of the intensity, scaled by species, of standard-confirmed iridoids through the five measured stages of maturation. MVA pathway: ACAT, acetyl coenzyme A (CoA) acetyltransferase; HMGS, hydroxymethylglutaryl-CoA synthase; HMGR, hydroxymethylglutaryl-CoA reductase; MK, mevalonate kinase; PMK, phosphomevalonate kinase; MDD, mevalonate diphosphate decarboxylase; isopentenyl diphosphate delta-isomerase (IDI). MEP pathway: DXS, 1-deoxy-D-xylulose-5-phosphate synthase; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase;MCT, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; CMK, 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol kinase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; HDS, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; HMDR, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase; GPPS, geranyl pyrophosphate synthase. Iridoid biosynthesis: GES, geraniol synthase; G8H, geraniol 8-hydroxylase; 8HGO, 8-hydroxygeraniol oxidoreductase; ISY, iridoid synthase; ISP, iridoid synthase paralogue; IO, iridoid oxidase; 7DLGT, 7-deoxyloganetic acid glucosyltransferase; 7eLAS, 7- epi -loganic acid synthase; 7eLAMT, 7- epi -loganic acid O-methyltransferase; OMES, oleoside methyl ester synthase; OMEGT, oleoside-11-methyl ester glucosyl transferase; OS, oleuropein synthase.

Article Snippet: The rest of the iridoid standards (7-deoxy-loganic acid, 7-deoxy-8- epi -loganic acid, 7-deoxy-loganin, 7-deoxy-8- epi -loganic acid, 7- epi -loganic acid, 7- epi -loganin, and 7-ketologanin) were synthesized from commercially available geniposide ( Biosynth Carbosynth , Staad, Switzerland) as previously reported ( ).

Techniques: Expressing, Transformation Assay, Standard Deviation