In order to profile the lipidome for untargeted lipidomics applications, analysis by ultra-high performance liquid chromatography – high resolution mass spectrometry (UHPLC-HRMS) typically requires ...the extraction of lipid content from sample matrices using matrix-specific conditions. The Folch, Bligh-Dyer, and Matyash extraction methods, while promising approaches, were originally tailored to specific matrices (brain tissue, fish muscle, and E. coli, respectively). Each of these methods have specific solvent ratios that must be adhered to achieve optimal extraction. Thus, the sample-to-solvent ratios for these methods should be optimized for the sample matrix of interest prior to employment. This study evaluated the appropriate sample-to-extraction solvent ratios for human plasma-based lipidomics studies. An advantage of employing biphasic lipid extractions is the ability to investigate both the aqueous and organic layers for increased analyte coverage in untargeted studies. Therefore, this work also evaluated the multi-omic capability of each lipid extraction method for plasma in an effort to provide a workflow capable of increasing analyte coverage in a single extraction, thus providing a more complete understanding of complex biological systems. In plasma, a decrease in sample-to-solvent ratios from 1:4, 1:10, 1:20, to 1:100 (v/v) resulted in a gradual increase in the peak area of a diverse range of metabolite (aqueous layer) and lipid (organic layer) species for each extraction method up to the 1:20(v/v) sample-to-solvent ratio. The Bligh-Dyer and Folch methods yielded the highest peak areas at every plasma sample-to-solvent ratios for both metabolite and lipid species. Depending on the lipid class of interest, the Folch or Bligh-Dyer method is best suited for analysis of human plasma at a 1:20 (v/v) sample to total solvent ratio.
Display omitted
•Evaluated sample-to-solvent ratios for plasma lipid extractions.•Evaluated the applicability of plasma multi-omic analysis for the Bligh-Dyer, Folch, and Matyash lipid extraction methods.•Plasma sample-to-solvent ratios of 1:20 (v/v) are ideal for multi-omics analysis with the Folch and Bligh-Dyer methods.•The Folch and Bligh-Dyer (aqueous layer from the 1:20 (v/v) ratio) yielded similar results to an 80% methanol extraction.
Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with ...disease. Methods expanding coverage of the lipidome increase the likelihood of biomarker discovery and could lead to more comprehensive understanding of disease etiology.
We introduce LipidMatch, an R-based tool for lipid identification for liquid chromatography tandem mass spectrometry workflows. LipidMatch currently has over 250,000 lipid species spanning 56 lipid types contained in in silico fragmentation libraries. Unique fragmentation libraries, compared to other open source software, include oxidized lipids, bile acids, sphingosines, and previously uncharacterized adducts, including ammoniated cardiolipins. LipidMatch uses rule-based identification. For each lipid type, the user can select which fragments must be observed for identification. Rule-based identification allows for correct annotation of lipids based on the fragments observed, unlike typical identification based solely on spectral similarity scores, where over-reporting structural details that are not conferred by fragmentation data is common. Another unique feature of LipidMatch is ranking lipid identifications for a given feature by the sum of fragment intensities. For each lipid candidate, the intensities of experimental fragments with exact mass matches to expected in silico fragments are summed. The lipid identifications with the greatest summed intensity using this ranking algorithm were comparable to other lipid identification software annotations, MS-DIAL and Greazy. For example, for features with identifications from all 3 software, 92% of LipidMatch identifications by fatty acyl constituents were corroborated by at least one other software in positive mode and 98% in negative ion mode.
LipidMatch allows users to annotate lipids across a wide range of high resolution tandem mass spectrometry experiments, including imaging experiments, direct infusion experiments, and experiments employing liquid chromatography. LipidMatch leverages the most extensive in silico fragmentation libraries of freely available software. When integrated into a larger lipidomics workflow, LipidMatch may increase the probability of finding lipid-based biomarkers and determining etiology of disease by covering a greater portion of the lipidome and using annotation which does not over-report biologically relevant structural details of identified lipid molecules.
Phage-based biocontrol of foodborne Salmonella is limited by the requisite use of Salmonella to propagate the phages. This limitation can be circumvented by producing Salmonella phages using a ...cell-free gene expression system (CFE) with a non-pathogenic chassis. Here, we produce the Salmonella phage felixO1 using an E. coli-based CFE system.
•Simple method for obtaining high-concentration phage genomic DNA•Cell free expression of Felixounavirus bacteriophages•Escherichia coli based cell free expression of Salmonella specific phage
Per- and polyfluoroalkyl substances (PFAS) are an emerging class of toxic environmental contaminants. Over 7500 PFAS exist, but reference standards are available for less than 2% of compounds. ...Nontargeted analysis using liquid chromatography–high-resolution tandem mass spectrometry is therefore an essential technique for increasing the analytical coverage of PFAS present in environmental samples. However, typical nontargeted data analysis is laborious and has a steep learning curve. Recently, FluoroMatch, a new open source, vendor neutral software, was published specifically for automating data processing for nontargeted analysis of PFAS and generating PFAS libraries. Here, we analyze soil contaminated with PFAS based aqueous film forming foam (AFFF) and compare the results produced by data analysis workflows using FluoroMatch and Compound Discoverer, an established nontargeted analysis program. High-confidence PFAS annotations were nearly identical between the methods, with 27 out of 32 compounds found using both Compound Discoverer and the modular version of FluoroMatch. Twenty-two high-confidence annotations were found using the comprehensive FluoroMatch Flow. The FluoroMatch method was faster and required significantly less manual curation than the Compound Discoverer method. Both platforms produced high-quality data that were useful for assessing PFAS contamination in the soil.
Given the opposing responses reported for bisphenol A (BPA) in terms of induction of obesogenic effects and impaired lipid metabolism, the increasing use of bisphenol F (BPF), and the relatively low ...information available regarding the effects of bisphenol A bis(3-chloro-2- hydroxypropyl) ether (BADGE·2HCl) in aquatic organisms, this work aims to use the zebrafish liver cell line (ZFL) as an alternative model to characterize the toxicity and the lipid metabolism disruptive potential of the selected compounds in fish. All three bisphenols increased intracellular levels of dihydroceramides and ether-triacylglycerides (ether-TGs), suggestive of inhibited cell growth. However, while BPA and BADGE·2HCl caused an increase of saturated and lower unsaturated TGs, BPF caused oxidative stress and the decrease of TGs containing polyunsaturated fatty acids (PUFAs). Analysis by qPCR highlighted the up-regulation of the lipogenic genes scd and elovl6 by BPA and BPF in line with an increase of lipids containing saturated and monounsaturated FA and a decrease of lipids containing PUFAs. This study shows that BPA, BPF and BADGE·2HCl target lipid homeostasis in ZFL cells through different mechanisms, and highlights the higher lipotoxicity of BADGE·2HCl compared to BPA and BPF.
Display omitted
•BPA, BPF and BADGE·2HCl induced significant changes in the lipidome of ZFL cells.•All three compounds induced the intracellular accumulation of TGs and dihydroceramides.•BPF generated oxidative stress and a decrease in polyunsaturated lipids.•ZFL-based lipidomic studies are useful for the detection of lipid disrupters in fish.
Large volumes of per- and polyfluoroalkyl substances (PFAS)-contaminated wastewaters, such as municipal solid waste landfill leachates, pose a challenge for PFAS treatment technologies in practice ...today. In this study, the surfactant properties of PFAS were exploited to concentrate the compounds in foam produced via the bubble aeration of landfill leachate. The effectiveness of the foaming technique for concentrating PFAS varied by compound, with a mean removal percentage (the percent difference between PFAS in leachate before and after foam removal) of 69% and a median removal percentage of 92% among the 10 replicate foaming experiments. This technique appears to be similarly effective at sequestering sulfonates and carboxylate PFAS compounds and is less effective at concentrating the smallest and largest PFAS molecules. The results of this study suggest that for the pretreatment or preconcentration of landfill leachates, foaming to sequester PFAS may provide a practical approach that could be strategically coupled to high-energy PFAS-destructive treatment technologies. The process described herein is simple and could feasibly be applied at a relatively low cost at most landfills, where leachate aeration is already commonplace.
Thousands of per- and polyfluoroalkyl substances (PFAS) exist in the environment and pose a potential health hazard. Suspect and nontarget screening with liquid chromatography (LC)–high-resolution ...tandem mass spectrometry (HRMS/MS) can be used for comprehensive characterization of PFAS. To date, no automated open source PFAS data analysis software exists to mine these extensive data sets. We introduce FluoroMatch, which automates file conversion, chromatographic peak picking, blank feature filtering, PFAS annotation based on precursor and fragment masses, and annotation ranking. The software library currently contains ∼7 000 PFAS fragmentation patterns based on rules derived from standards and literature, and the software automates a process for users to add additional compounds. The use of intelligent data-acquisition methods (iterative exclusion) nearly doubled the number of annotations. The software application is demonstrated by characterizing PFAS in landfill leachate as well as in leachate foam generated to concentrate the compounds for remediation purposes. FluoroMatch had wide coverage, returning 27 PFAS annotations for landfill leachate samples, explaining 71% of the all-ion fragmentation (CF2) n related fragments. By improving the throughput and coverage of PFAS annotation, FluoroMatch will accelerate the discovery of PFAS posing significant human risk.
Cell and animal models have been used to provide insights with regard to physiological changes in intestinal flora due to exposure to drugs and environmental contaminants. Here, a novel in vitro ...model known as simulator of the human intestinal microbial ecosystem (SHIME) was used to assess the effects of three chemicals of emerging concern, namely glyphosate, perfluorooctanoic acid (PFOA), and docusate sodium (dioctyl sulfosuccinate, DOSS), on the lipidomic and metabolomic profiles of the gut microenvironment in both the proximal and distal colonic compartments. Nontargeted analyses by ultra-high performance liquid chromatography-tandem mass spectrometry and gas chromatography–electron ionization-mass spectrometry revealed minor differences in the lipidomic and metabolomic signatures of the proximal and distal colon following treatment with either glyphosate or PFOA at acceptable human daily intake levels or average daily exposures. However, global dysregulation of lipids and metabolites was observed due to DOSS treatment at conventional prescription doses when indicated as a stool softener. Our findings suggest that the current guidelines for glyphosate and PFOA exposure may be adequate at the level of the lower gut microbiome in healthy adults, but the probable yet uncharacterized off-target effects, safety, and efficacy of long-term DOSS treatment warrants further investigation. Indeed, we highlight the SHIME system as a novel in vitro approach which can be used as a screening tool to assess the impact of drugs and/or chemicals on the gut microbiome, while implementing state-of-the-art and data-driven mass spectrometric workflows to identify toxic lipidomic and metabolomic signatures.
As regulatory frameworks for per- and polyfluoroalkyl substances (PFAS) evolve, the solid waste community seeks to manage PFAS risks effectively. Despite extensive research on PFAS in municipal solid ...waste (MSW) and wastewater sludge, there is limited information on a major global waste stream which seldom gleans regulatory oversight — construction and demolition debris (CDD). This study sampled a CDD processing facility to provide material-specific information on the PFAS profile within CDD. The bulk CDD accepted by this facility was separated into major categories, representatively sampled, then characterized for total available PFAS (∑92PFAS). As reprocessed CDD is ultimately recycled or landfilled, often unencapsulated or in unlined landfills, the PFAS leaching potential was also examined using two leaching procedures. Among the categories assessed for total PFAS, carpeting, carpet padding, and gypsum drywall showed elevated concentrations compared to other components, with most of the PFAS mass contributed by precursor species. However, materials with the highest total PFAS, such as carpeting, did not necessarily exhibit the highest leaching, and leachate was predominantly composed of terminal species rather than precursors. Extrapolating these findings with national CDD generation and management data inventories suggests that despite MSW having higher total available PFAS concentrations, the leachability of PFAS from landfilled CDD is comparable, raising legitimate concerns with CDD disposal practices, particularly in unlined CDD landfills.
Display omitted
•Various PFAS levels detected in CDD components.•Majority of total available PFAS was from precursor species.•Leachable PFAS consisted mainly of PFCAs.•Data were extrapolated to estimate US CDD waste PFAS mass.•CDD may pose similar or greater leaching risk compared to MSW.
PDF
