Biology subjects

Fleming, J. F.

Publications and source records attributed to Fleming, J. F..

2 recordsLinked to original sources

bioRxiv2025

Updated Guidance for Communicating PFAS Identification Confidence with Ion Mobility Spectrometry

Over the last decade, global contamination from per- and polyfluoroalkyl substances (PFAS) has become apparent due to their detection in countless matrices worldwide, from consumer products to human blood to drinking water. As researchers implement non-targeted analyses (NTA) to more fully understand the PFAS present in the environment and human bodies, clear guidance is needed for consistent and objective reporting of the identified molecules. Confidence levels for small molecules analyzed and identified with high-resolution mass spectrometry (HRMS) have existed since 2014; however, unification of currently-used levels and improved guidance for their application is needed due to inconsistencies in reporting and continuing innovations in analytical methods. Here, we (i) investigate current practices for confidence level reporting of PFAS identified with liquid chromatography (LC), gas chromatography (GC), and/or ion mobility spectrometry (IMS) coupled with HRMS and (ii) propose a simple, unified confidence level guidance that incorporates both PFAS-specific attributes and IMS collision cross section (CCS) values. SynopsisUnified and simplified requirements to guide confidence level assignment in non-targeted PFAS identification efforts with ion mobility spectrometry. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/634925v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1b9808dorg.highwire.dtl.DTLVardef@1a6e663org.highwire.dtl.DTLVardef@5f8813org.highwire.dtl.DTLVardef@1dea0d1_HPS_FORMAT_FIGEXP M_FIG For Table of Contents only C_FIG

scientific communication and education↗

bioRxiv2023

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations1. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution2, 3. However, the veracity and timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved4-6 and whether these WGD events underlie vertebrate phenotypic diversification remains elusive7. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage in the late Cambrian after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced two additional, independent genome duplications (herein CR1 and CR2). Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of morphological complexity7.

genomics↗