Towards detecting genotoxic chemicals in food packaging at thresholds of toxicological concern using bioassays with high-performance thin-layer chromatography

High-performance thin-layer chromatography (HPTLC)-bioassays are promising new methods for detecting bioactive chemicals in food packaging. Here, we test whether direct-acting genotoxic chemicals are detectable in food contact materials (FCM) using HPTLC-bioassays. First, an interactive worksheet lays out steps to calculate needed detection limits in (bio)analytical methods from regulatory limits, including thresholds of toxicological concern (TTC). Second, we show that the sensitivity of a HPTLC-genotoxicity assay to low doses of chemicals, including food contact chemicals, is greater than a standardized microtiter plate version and in vitro assays already reported. Third, using HPTLC, we detected genotoxicity in extracts of FCM, and not in simulated migrates of FCM. Applying the worksheet to calculate needed detection limits in FCM migrates, we observed that seven of ten genotoxic chemicals would be detectable with HPTLC if present at the regulatory 10 ppb limit and two of ten at TTC for adults. With development, HPTLC-bioassays might become the best option for supporting safety assessment of genotoxicants in food packaging

High-Coverage Nanopore Sequencing of Samples From the 1000 Genomes Project To Build a Comprehensive Catalog of Human Genetic Variation

Fewer than half of individuals with a suspected Mendelian or monogenic condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control data sets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project (1KGP) Oxford Nanopore Technologies Sequencing Consortium aims to generate LRS data from at least 800 of the 1KGP samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37× and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs

Enhanced MALDI Ionization Efficiency at the Metal-Matrix Interface: Practical and Mechanistic Consequences of Sample Thickness and Preparation Method

Electrosprayed spots of varying thickness were evaluated for use as reproducible, homogenous, high efficiency MALDI samples. Thin samples on stainless steel plates were found to give exceptionally strong signals, as did the last layers of thick samples, when ablated down to the steel substrate. A small enhancement was also observed for thin samples on a gold substrate, and with a few-nanometer gold coating on top of a thick sample. Ion yields and intensity ratios can be understood in the context of the previously described quantitative MALDI model including the matrix-metal interfacial ionization potential reduction effect (Knochenmuss, R.; Anal. Chem. 2004, 76, 3179–3184). The absolute and relative stabilities of ion signals were found to be at least a factor of two better for the thin electrosprayed spots, compared to spots prepared by dried droplet methods

Small-molecule MALDI using the matrix suppression effect to reduce or eliminate matrix background interferences.

The matrix suppression effect (MSE) can lead to high-quality MALDI mass spectra: strong analyte signals and weak or negligible matrix background peaks. Experiment and theory suggest that MSE should be widespread and, therefore, generally applicable to measurement of low molecular weight (LMW) substances. These are otherwise impractical with MALDI due to interference from matrix. Appropriate conditions for MSE were investigated and tested on a variety of LMW substances. Straightforward and semiautomated interpretation was possible for 87.7% of these. Another 3.5% gave poor MSE due to sodium cationization rather than protonation of the analyte, but interpretation was possible. MALDI imaging shows that MSE varies significantly across a typical sample. Selective data accumulation could further increase the utility of the method. Samples containing more than one analyte were also studied. Analyte-analyte suppression was not found to be excessive, and moderately abundant minority species can be adequately detected