Naphthenic acids (NAs) are naturally occurring in the Athabasca oil sands region (AOSR) and accumulate in tailings as a result of water-based extraction processes. NAs exist as a complex mixture, so the development of an analytical technique to characterize them has been an on-going challenge. The aim of this study was to use comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry to monitor individual NAs within a wetland reclamation site in the AOSR. Samples were collected from four monitoring wells at the site and the extracts were found to contain numerous resolved isomers of classical (monocyclic-, bicyclic-, adamantane-, indane-, and tetralin-type carboxylic acids) and sulfur-containing NAs (thiamonocyclic- and thiophene-type carboxylic acids). The absolute abundances of the monitored NAs were compared between four monitoring wells and unique profiles were observed at each well. Few significant changes in absolute abundances were observed over the sampling period, with the exception of one well (Well 6A). In addition, isomeric percent compositions were calculated for each set of structural isomers, and one-way analysis of variance (ANOVA) and two-dimensional hierarchical cluster analysis revealed high spatial variation at the site. However, consistent distributions were observed at each of the monitoring wells for some sets of NA isomers (such as: adamantane NAs), which may be useful for forensic applications, such as identifying sources of contamination or demonstrating biodegradation. The methods and results presented in this study demonstrate the utility of monitoring individual NAs, since both changes in absolute abundances of individual NAs and the distribution of NA isomers have the ability to provide insight into their sources and the processes controlling their concentrations that are not only of relevance to the Alberta Oil Sands, but also to other petroleum deposits and environmental systems.

This study reports the first application of comprehensive two-dimensional gas chromatography coupled to a high-resolution quadrupole time-of-flight mass spectrometer (GC×GC/HRQTOF-MS) for the characterization of naphthenic acid fraction compounds (NAFCs) from the Alberta Oil Sands. High resolution mass spectrometry (HRMS) significantly increased the coverage of NAFCs in the mixture and allowed the differentiation of NAFCs from several chemical classes. It was demonstrated that GC×GC, in combination with the high mass accuracy and precision of the HRQTOF-MS, could distinguish chemical species with the C3 vs SH4 mass split at a much lower resolving power than required with direct infusion experiments. Mass defect plots were useful for visualizing the complex datasets generated by GC×GC/HRQTOF-MS and led to the identification of 1105 chemical species with unique elemental compositions (<5ppm mass accuracy). Mass defect plots were shown to be a powerful screening tool and enabled the detection of extensive isomer series from the SO2 chemical class, some of which have not been previously reported in oil sands related samples. The GC×GC/HRQTOF-MS approach is expected to improve NAFC monitoring programs since the technique allows the qualitative analysis of individual NAFCs and provides unique fingerprints via isomer distributions which may assist in future fingerprinting studies.

Streptococcus intermedius, S. constellatus, and S. anginosus comprise the Streptococcus Milleri/Anginosus group (SMG). They are facultative anaerobic bacteria that asymptomatically colonize the upper respiratory, gastrointestinal and urogenital tracts. They are also common pathogens in pyogenic invasive infections, as well as pulmonary and urinary tract infections. Most SMG infections are polymicrobial and associated with co-infecting obligate anaerobic bacteria. To better understand the effect of oxygen on the growth and physiology of these organisms, we compared the global metabolomic and transcriptomic profiles of S. intermedius strain B196 under aerobic and anaerobic conditions. The largest transcriptional changes were associated with induction of oxidative stress response genes under aerobic conditions. Modest changes in expression of genes associated with primary metabolism were observed under the two conditions. Intracellular and extracellular metabolites were measured using HILIC–LCMS. Differences in the abundance of specific metabolites were correlated with observed transcription changes in genes associated with their metabolism, implying that metabolism is primarily regulated at the transcriptional level. Rather than a large shift in primary metabolism under anaerobic conditions our results suggest a modest tuning of metabolism to support the accelerated growth rate of S. intermedius strain B196 in the absence of oxygen. For example, under anaerobic conditions, purine metabolism, pyrimidine de novo synthesis and pyrimidine salvage pathways were up-regulated at metabolic and transcriptional levels. This study provides a better understanding of differences between S. intermedius anaerobic and aerobic metabolism. The results reflect the organism’s predilection for anaerobic growth consistent with its pathogenic association with anaerobes in polymicrobial infections.

Suspended sediment quality in Hamilton Harbour has been assessed as part of a long-term monitoring study (1987–2012). Sampling locations reflected a range of shoreline activities and sources of chemical contamination to the harbour. Temporal data showed a trend toward decreasing levels of contamination by polycyclic aromatic hydrocarbons and polychlorinated biphenyls over the period from the late 1980s to the early 1990s, with a subsequent leveling off over the next two decades. The highest concentrations of both contaminants were detected in areas impacted by industrial activities along the southern shoreline and Windermere Arm, and deep-water areas of the harbour where fine-grained sediments ultimately accumulate. Areas of the harbor discharging residential or rural parts of the watershed exhibited generally lower levels of contamination. In addition to the relatively higher contaminant levels, areas along the southern shoreline and Windermere Arm characterized by historical industrial activities and associated contaminated sediments exhibited chemical profiles indicating an impact on suspended sediment and bottom sediment quality throughout the harbour. Continued monitoring after scheduled remedial activities should provide an assessment of the overall efficacy of management actions to improve sediment quality in Hamilton Harbour.

Macrophages are major contributors to age-associated inflammation. Metabolic processes such as oxidative phosphorylation, glycolysis and the urea cycle regulate inflammatory responses by macrophages. Metabolic profiles changes with age; therefore, we hypothesized that dysregulation of metabolic processes could contribute to macrophage hyporesponsiveness to LPS. We examined the intracellular metabolome of bone marrow-derived macrophages from young (6–8 wk) and old (18–22 mo) mice following lipopolysaccharide (LPS) stimulation and tolerance. We discovered known and novel metabolites that were associated with the LPS response of macrophages from young mice, which were not inducible in macrophages from old mice. Macrophages from old mice were largely non-responsive towards LPS stimulation and we did not observe a shift from oxidative phosphorylation to glycolysis. The critical regulatory metabolites succinate, γ-aminobutyric acid, arginine, ornithine and adenosine were increased in LPS-stimulated macrophages from young mice, but not macrophages from old mice. A shift between glycolysis and oxidative phosphorylation was not observed during LPS tolerance in macrophages from either young or old mice. Metabolic bottlenecks may be one of the mechanisms that contribute to the dysregulation of LPS responses with age.

A comprehensive method to extract perfluoroalkane sulfonic acids (PFSAs), perfluoroalkyl carboxylic acids (PFCAs), polyfluoroallcyl phosphoric acid diesters (diPAPs), perfluoroalkyl phosphinic acids (PFPiAs) and perfluoroalkyl phosphonic acids (PFPAs) from sediment and analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) was developed and applied to sediment cores from three small isolated lakes (Plastic Lake, lake 442, Lake Tettegouche) and Lake Ontario in the Great Lakes Region. Recoveries of the target compounds using the optimized acetonitrile/sodium hydroxide extraction ranged from 73% to 120%. The greatest concentrations of per- and polyfluorinated alkyl substances (PFASs) were recorded in sediment from Lake Ontario (Sigma PFASs 13.1 ng/g), where perfluorooctane sulfonic acid (PFOS) contributed over 80% of the total. Concentrations in Lake Ontario were approximately 1-2 orders of magnitude greater than the more remote lakes subject to primarily atmospheric inputs. Whilst the PFAS contribution in Lake Ontario was dominated by PFOS, the more remote lakes contained sediment with higher proportions of PFCAs. Trace amounts of emerging PFASs (diPAPs and PFPiAs) were found in very recent surface Lake Ontario and remote lake sediments. (C) 2016 Elsevier Ltd. All rights reserved.

Smoke from wood-fueled fires is one of the most common hazards encountered by firefighters worldwide. Wood smoke is complex in nature and contains numerous compounds, including methoxyphenols (MPs) and polycyclic aromatic hydrocarbons (PAHs), some of which are carcinogenic. Chronic exposure to wood smoke can lead to adverse health outcomes, including respiratory infections, impaired lung function, cardiac infarctions, and cancers. At training exercises held in burn houses at four fire departments across Ontario, air samples, skin wipes, and urine specimens from a cohort of firefighters (n = 28) were collected prior to and after exposure. Wood was the primary fuel used in these training exercises. Air samples showed that MP concentrations were on average 5-fold greater than those of PAHs. Skin wipe samples acquired from multiple body sites of firefighters indicated whole-body smoke exposure. A suite of MPs (methyl-, ethyl-, and propylsyringol) and deconjugated PAH metabolites (hydroxynaphthalene, hydroxyfluorene, hydroxyphenanthrene, and their isomers) were found to be sensitive markers of smoke exposure in urine. Creatinine-normalized levels of these markers were significantly elevated (p < 0.05) in 24 h postexposure urine despite large between-subject variations that were dependent on the specific operational roles of firefighters while using personal protective equipment. This work offers deeper insight into potential health risk from smoke exposure that is needed for translation of better mitigation policies, including improved equipment to reduce direct skin absorption and standardized hygiene practices implemented at different regional fire services.

The soil bacterium Sinorhizobium meliloti forms nodules on the roots of leguminous plants, where N2 is reduced to ammonia. Its genome includes a 3.65 Mb chromosome, a 1.35 Mb pSymA megaplasmid, and a 1.68 Mb pSymB chromid. pSymA and pSymB constitute ~45 % of the genome and here a non-targeted approach was used to identify the metabolic consequences of the removal of these replicons. Polar and non-polar metabolites from wild-type, ∆pSymA, ∆pSymB, and ∆pSymAB cells and supernatants across a growth curve were analyzed by LC–HILIC–TOF–MS. 2008 metabolite features were identified in the extracellular metabolome of cells grown in LBmc containing yeast extract and casein hydrolysate. 1474 features were found from the intracellular metabolites of cells grown in minimal M9-sucrose medium. Analysis revealed both time and genotype influenced the metabolome, with the removal of pSymB having a much greater effect than the loss of pSymA. Strains lacking pSymB showed an increase in sugar, amino acid, and nucleotide metabolites in the intracellular metabolome, and the loss of pSymB clearly impaired the cell’s ability to catabolize exogenous amino acids. We conclude that despite the ability of wild-type, ∆pSymA, ∆pSymB, and ∆pSymAB strains to grow in both M9-sucrose and LBmc media, the removal of pSymA, and particularly pSymB, had clear and dramatic effects on the S. meliloti metabolome. The larger effect associated with the pSymB chromid is consistent with the large number of metabolic genes on this replicon and the greater genetic and metabolic integration of this replicon with the S. meliloti chromosome.

The environmental occurrence of dechlorination moieties from the high production volume flame retardant, Dechlorane Plus (DP), has largely been documented; however, the sources have yet to be well understood. In addition, few laboratory-based studies exist which identify the cause for the occurrence of these chemicals in the environment or humans. Anaerobic dechlorination of the two DP isomers was investigated using a laboratory-simulated wastewater treatment plant (WWTP) environment where anaerobic digestion is used as part of the treatment regime. Known amounts of each isomer were added separately to sewage sludge which provided the electron-donating substrate and at prescribed time points in the incubation, a portion of the media was removed and analyzed for DP and any dechlorination metabolites. After 7 days, monohydrodechlorinated products were observed for both the syn- and anti-DP which were continued throughout the duration of our study (49 days) in an increasing manner giving a calculated formation rate of 0.48 ± 0.09 and 0.79 ± 0.12 pmols/day for syn- and anti-DP, respectively. Furthermore, we observed a second monohydrodechlorinated product only in the anti-DP isomer incubation medium. This strongly suggests that anti-DP is more susceptible to anaerobic degradation than the syn isomer. We also provide compelling evidence to the location of chlorine loss in the dechlorination DP analogues. Finally, the dechlorination DP moieties formed in our study matched the retention times and identification of those observed in surficial sediment located downstream of the WWTP.

A fungal endophyte isolated from a Concord grape leaf led to the discovery of new diplosporin and agistatine derivatives.

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

A comprehensive approach was taken to characterize the polyhalogenated dibenzo-p-dioxin and dibenzofuran contents of fire debris. Household and electronics fire simulations were performed to create samples representative of those firefighters most typically come in contact with. Sample analysis was performed using GC×GC-TOFMS to provide a comprehensive profile of the halogenated dioxins and furans present among the two types of fire debris. Both the household fire and electronics fire simulations produced a significant amount of polybrominated dibenzofurans. Only the electronics rich fire simulation produced mixed halogenated (Br/Cl) dibenzofurans in amounts above the limit of detection of the analytical method. Of the mixed halogenated dibenzofurans identified, a majority were those having no commercially available standard to allow for specific congener identification. GC×GC-TOFMS was extremely beneficial for the identification of compound classes due to the manner in which compounds classify in the two-dimensional chromatographic plane, thus aiding data reduction for these materials.

RATIONALE: Naphthenic acids (NAs) accumulate in oil sands process-affected water (OSPW) as a result of the water-based extraction processes, and represent one of the toxic fractions in OSPW. They exist as a complex mixture and so the development of an analytical method to characterize and quantify individual acids has been an on-going challenge. The multidimensional separation technique of two-dimensional gas chromatography (GC x GC) has the potential to provide a fingerprint of the sources of NAs and can potentially resolve individual analytes for target analysis. However, the identity and toxicity of a large proportion of the acids present in tailing waters are still unknown.METHODS: Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GCxGC/TOFMS) was used to characterize NAs in a pore water sample from a Syncrude composite tailings (CT) deposit in Fort McMurray, Alberta, Canada. The extractable organic acid fraction was derivatized with diazomethane and the structures of selected resolved esters were elucidated through interpretation of their electron ionization (EI) mass spectra and, if available, confirmed by comparison with the spectra of reference standards.RESULTS: The high resolving power of the GCxGC/TOFMS technique allowed for the structural elucidation of numerous as yet unidentified acids in the CT pore water sample such as carboxylic acids containing a thiophene, indane, tetralin or cyclohexane moiety. Seventeen members of the previously reported class of adamantane-type carboxylic acids in oil sands process water could also be identified in the sample.CONCLUSIONS: This study underlines the complexity of naphthenic acid isomer distributions in composite tailings and provides a useful inventory of individual acids. Copyright (C) 2014 John Wiley & Sons, Ltd.

Acute anaphylaxis caused by food allergy is a potentially life-threatening allergic reaction that results in thousands of hospitalizations in North America every year. There are currently no effective means of treatment for anaphylaxis beyond the administration of epinephrine which is only given after a reaction has already started. Furthermore, knowledge regarding the underlying physico-chemical basis of anaphylaxis is largely incomplete. Arguably, the study of anaphylaxis by comprehensive metabolomics offers a unique opportunity to study this phenomenon due to its ability to provide a snap-shot of the chemical state of a subject experiencing anaphylaxis encompassing both endogenous and exogenous factors including dietary and environmental effects. In this study, we sought to apply a comprehensive metabolomics approach using liquid chromatography–mass spectrometry to a murine model of peanut-induced anaphylaxis. The results of this study revealed that the metabolomic profiles of mice experiencing peanut-induced anaphylaxis followed a distinct pattern that mirrors the time-stage of anaphylaxis being experienced. Direct comparison of anaphylactic mice to time-matched control mice showed that the metabolomic profiles changed considerably as the anaphylactic reaction progressed. This comparison also revealed changes in both known biomarkers of anaphylaxis such as histamine and methylhistamine as well as a suite of metabolites chemically similar to known anaphylaxis mediators but whose biological functions are not well understood. These metabolites include a number of phospholipids such as a variety of phosphatidylcholines and lyso-phosphatidylcholines that may be of interest for further investigation regarding their potential as anaphylaxis mediators or chemical precursors to mediators.

Between July 9-12, 1997, at least 400 tonnes of polyvinyl chloride (PVC) were consumed in a fire at the Plastimet Inc. plastics recycling facility in Hamilton, Ontario, Canada. This led to the release of contaminants, including highly toxic polychlorinated dibenzo-p-dioxins (PCDD) and dibenzofurans (PCDF). This study re-examines a composite soil sample collected shortly after the fire using state-of-the-art FT-ICR (Fourier transform ion cyclotron resonance) and GC × GC-TOF (comprehensive two-dimensional gas chromatography-time-of-flight) mass spectrometry. The FT-ICR experiments led to the identification of approximately 150 molecular formulas, corresponding to chlorinated and mixed chloro/bromo compounds. The majority of these are halogenated polycyclic aromatic hydrocarbons (halo-PAHs), including highly substituted (e.g., C14HCl9 and C16HCl9) and high molecular weight (e.g., C28H12Cl4) Cl-PAHs that have not been reported previously in environmental samples. Complementary GC × GC-TOF experiments resolved individual halo-PAHs, some of which were confirmed with available standards. The concentrations of the most abundant halo-PAH groups, C14H8Cl2 (22 μg/g) and C16H8Cl2 (20 μg/g) are much higher than reported dioxin values and comparable to the corresponding PAH groups C14H10 (12 μg/g) and C16H10 (19 μg/g). The high abundance of the halo-PAHs identified in this study highlights the need for further investigation into their environmental occurrence and risk.

The ontogeny of peanut allergy (PA) remains poorly understood. We argued that an untargeted metabolomic analysis would be a useful hypothesis-generating tool to identify novel biomarkers, mediators and possibly therapeutic targets in PA. Models of PA and anaphylaxis used in this study involved either the oral administration of peanut along with cholera toxin or the topical application of peanut on tape-stripped skin. Liquid-chromatography mass-spectrometry (LC-MS) was performed to identify chemical changes in the serum of mice undergoing sensitization and anaphylaxis. Flow cytometry as well as in vivo gain-of-function and loss-of-function immunological studies were used to determine the biological significance of particular molecules in sensitization. LC-MS followed by multivariant analysis showed that the purine metabolism pathway was altered with elevated levels of uric acid (UA) in sensitized mice. UA depletion using allopurinol and uricase fully prevented the development of peanut-specific antibodies and the development of anaphylaxis. Conversely, administration of UA crystals, either orally or subcutaneously, instead of cholera toxin or tape-stripping, respectively, along with peanut induced allergic sensitization and anaphylactic phenotype. The immunostimulatory effect of UA and UA crystals is likely mediated through the activation of resident dendritic cells. We identified UA, released after damage to the mucosa and/or skin, as a critical alarmin that facilitates the development of peanut allergy and anaphylaxis.

The comprehensive metabolomic analyses using eukaryotic and prokaryotic cells are an effective way to identify biomarkers or biochemical pathways which can then be used to characterize disease states, differences between cell lines or inducers of cellular stress responses. One of the most commonly used extraction methods for comprehensive metabolomics is the Bligh and Dyer method (BD) which separates the metabolome into polar and nonpolar fractions. These fractions are then typically analysed separately using hydrophilic interaction liquid chromatography (HILIC) and reversed-phase (RP) liquid chromatography (LC), respectively. However, this method has low sample throughput and can also be biased to either polar or nonpolar metabolites. Here, we introduce a MeOH/EtOH/H2O extraction paired with HILIC-time-of-flight (TOF)-mass spectrometry (MS) for comprehensive and simultaneous detection of both polar and nonpolar metabolites that is compatible for a wide array of cellular species cultured in different growth media. This method has been shown to be capable of separating polar metabolites by a HILIC mechanism and classes of lipids by an adsorption-like mechanism. Furthermore, this method is scalable and offers a substantial increase in sample throughput compared to BD with comparable extraction efficiency. This method was able to cover 92.2% of the detectable metabolome of Gram-negative bacterium Sinorhizobium meliloti, as compared to 91.6% of the metabolome by a combination of BD polar (59.4%) and BD nonpolar (53.9%) fractions. This single-extraction HILIC approach was successfully used to characterize the endometabolism of Gram-negative and Gram-positive bacteria as well as mammalian macrophages.

The tandem use of hydrophilic interaction LC columns with RP columns in series configuration has resulted in the retention of both polar and nonpolar components in complex biological samples (mouse serum) in a single analysis. This approach successfully coupled various columns with orthogonal separation characteristics, employed a single solvent gradient program compatible with the two columns and used ESI coupled to a TOF mass spectrometer for detection. Ion suppression, a common problem in ESI, was virtually eliminated for components eluting with apparent capacity factors >0.7. Retention time reproducibility with the tandem columns performed over three days with over 100 injections was comparable to that observed for single columns alone. This method was applied to the analysis of a pooled mouse serum sample and afforded highly reproducible data for up to 3000 mass spectral features. This approach was implemented with a conventional LC-MS system and should find broad applicability in the comprehensive analysis of complex mixtures containing a wide range of compound polarities.