Honey bee collected pollen for botanical identification via its2 metabarcoding: a comparison of preservation methods for citizen science

DNA metabarcoding is emerging as a powerful method for botanical identification of bee-collected pollen, allowing analysis of hundreds of samples in a single high-throughput sequencing run, therefore offering unprecedented scale in citizen science projects. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is the first step of the pipeline. Hence, it is important to test whether the pollen preservation method influences metabarcoding performance. While in metabarcoding studies pollen has typically been preserved at −20°C, this is not the best method to be applied by citizen scientists. Here, we compared the freezing method (FRZ) with ethanol (EtOH), silica gel (SG) and room temperature (RT) in 87 pollen samples collected from hives in Austria and Denmark.AQ acknowledges the PhD scholarship (DFA/BD/5155/2020) funded by FCT. This study was funded by INSIGNIA “Environmental monitoring of pesticides use through honey bees” (SANTE/E4/SI2.788418-SI2.788452).info:eu-repo/semantics/publishedVersio

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Real-Time Measurement of Volatile Chemicals Released by Bed Bugs during Mating Activities

<div><p>In recent years, bed bug (Hemiptera: Cimicidae) problems have increased dramatically in many parts of the world, leading to a renewed interest in their chemical ecology. Most studies of bed bug semiochemicals have been based on the collection of volatiles over a period of time followed by chemical analysis. Here we present for the first time, a combination of proton transfer reaction mass spectrometry and video analysis for real-time measurement of semiochemicals emitted by isolated groups of bed bugs during specific behavioural activities. The most distinct peaks in the proton transfer reaction mass spectrometry recordings were always observed close to the termination of mating attempts, corresponding to the defensive emissions that bed bugs have been suspected to exploit for prevention of unwanted copulations. The main components of these emissions were (<em>E</em>)-2-hexenal and (<em>E</em>)-2-octenal recorded in ratios between 1∶3 and 3∶1. In the current study, the quantity varied over 1000 fold for both of the compounds with up to 40 µg total release in a single emission. Males also emit defensive compounds due to homosexual copulation attempts by other males, and no significant differences were observed in the ratio or the amount of the two components released from males or females. In summary, this study has demonstrated that combining proton-transfer-reaction mass spectrometry with video analysis can provide detailed information about semiochemicals emitted during specific behavioural activities.</p> </div

Example of aldehyde emissions and correlation with behavioural observation.

<p>Results from a PTR-MS recording on four male and four female bed bugs. The thick horizontal lines indicate mating attempts of male on female (red), male on male (blue) or a second male trying to copulate an already established male-female couple (orange). A. Estimated concentrations of (<i>E</i>)-2-hexenal and (<i>E</i>)-2-octenal over the entire recording period. B. Observed (dashed black line) and calculated (green line) ion counts for the mass 57 which is produced from both (<i>E</i>)-2-hexenal and (<i>E</i>)-2-octenal.</p

Doses of (<i>E</i>)-2-hexenal and (<i>E</i>)-2-octenal in individual emissions.

<p>All observations are based on PTR-MS recordings combined with video recordings. The dashed line indicates equal amounts of (<i>E</i>)-2-hexenal and (<i>E</i>)-2-octenal. The ratio of (<i>E</i>)-2-hexenal and (<i>E</i>)-2-octenal released during the three types of copulation formations were not significantly different from one (♂-♀: <i>t</i>₉ = 1.30; <i>P</i> = 0.23; ♂-♂: <i>t</i>₂₈ = −1.09; <i>P</i> = 0.28; ♂-♀-♂: <i>t</i>₂ = 0.53; <i>P</i> = 0.65).</p

Examples of aldehyde emissions and correlation with behavioural observations.

<p>Results from two PTR-MS recordings on either eight males (A) or four males and four females (B). The thick horizontal lines indicate mating attempts of male on female (red), male on male (blue) or a second male trying to copulate an already established male-female couple (orange). The amount of (<i>E</i>)-2-hexenal and (<i>E</i>)-2-octenal emitted over the entire experimental period of A is also shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050981#pone-0050981-t002" target="_blank">Table 2</a>. In B, the bed bugs were kept in the closed experimental container without access to blood during the first 14 minutes (until the first arrow), then the container was placed on the arm of a human volunteer and the bed bugs were allowed to feed for the last 12 minutes (from the second arrow).</p

Examples of individual TD GC-MS and PTR-MS recordings.

<p>n.d.: Not found or below detection limit.</p><p>Estimated amount of (<i>E</i>)-2-hexenal and (<i>E</i>)-2-octenal (in ng) emitted in the individual experiments illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050981#pone-0050981-g002" target="_blank">Fig. 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050981#pone-0050981-g003" target="_blank">3</a>. No TD GC-MS recording was available for the experiment shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050981#pone-0050981-g002" target="_blank">Fig. 2B</a>.</p