mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis.

We introduce mirTarRnaSeq, an R/Bioconductor package for quantitative assessment of miRNA-mRNA relationships within sample cohorts. mirTarRnaSeq is a statistical package to explore predicted or pre-hypothesized miRNA-mRNA relationships following target prediction.We present two use cases applying mirTarRnaSeq. First, to identify miRNA targets, we examined EBV miRNAs for interaction with human and virus transcriptomes of stomach adenocarcinoma. This revealed enrichment of mRNA targets highly expressed in CD105+ endothelial cells, monocytes, CD4+ T cells, NK cells, CD19+ B cells, and CD34 cells. Next, to investigate miRNA-mRNA relationships in SARS-CoV-2 (COVID-19) infection across time, we used paired miRNA and RNA sequenced datasets of SARS-CoV-2 infected lung epithelial cells across three time points (4, 12, and 24 hours post-infection). mirTarRnaSeq identified evidence for human miRNAs targeting cytokine signaling and neutrophil regulation immune pathways from 4 to 24 hours after SARS-CoV-2 infection. Confirming the clinical relevance of these predictions, three of the immune specific mRNA-miRNA relationships identified in human lung epithelial cells after SARS-CoV-2 infection were also observed to be differentially expressed in blood from patients with COVID-19. Overall, mirTarRnaSeq is a robust tool that can address a wide-range of biological questions providing improved prediction of miRNA-mRNA interactions.

Characterization and aging study of currency ink and currency canine training aids using headspace SPME/GC-MS.

Solid-phase microextraction/gas chromatography-mass spectrometry (SPME/GC-MS) was used to characterize the volatile components associated with U.S. currency, U.S. currency inks, and Canadian currency. Compounds that can be attributed to the ink-curing process include series of straight-chain aldehydes, alkenals, acids, alcohols, and ketones and a series of lactones and 2-alkyl furans. Solvent compounds include naphthenic and paraffinic hydrocarbons with a profile typical of petroleum products, alkyl cyclohexanes, various ethylene glycol alkyl ethers, and traces of chlorinated solvents. Trace levels of 2-phenoxyethanol, a solvent often used in ink formulations, were also detected. Environmental contaminants, those compounds found in circulating currency but not in currency ink, include 2,2'-diethyl-1,1'-biphenyl, methyl benzoate and salicylate, menthol, limonene, dimethyl and diethyl phthalate, and ionol. Not including simple hydrocarbons, over 100 compounds were identified in the headspace of currency-related samples.