Quantitative Analysis of Polycyclic Aromatic Hydrocarbons at Part Per Billion Levels in Fish Oil by Headspace Solid-Phase Microextraction and Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS).

Headspace solid-phase microextraction (HS-SPME) was used in combination with gas chromatography-mass spectrometry (GC-MS) for the analysis of polycyclic aromatic hydrocarbons (PAH) at part per billion levels in fish oil samples collected from menhaden fish. The method was initially developed using fish oil from capsules spiked with a standard PAH mixture. The final HS-SPME-GC-MS method presented a linear range from 3 to 1,500 ng/g, with precision for most analytes <10% relative standard deviation. The limits of detection varied from 1 to 7 ng/g depending on the analyte. Real sample analysis was done on menhaden fish oil extracted from fish collected off the coasts of New Jersey and Louisiana. Naphthalene, fluorene, fluoranthene, pyrene, anthracene were detected at low levels of 70-180 ng/g in the real samples. The concentrations of PAHs detected in the real samples were well below established levels of concern for PAHs in finfish.

Comparison of De Novo Transcriptome Assemblers and k-mer Strategies Using the Killifish, Fundulus heteroclitus.

BACKGROUND: De novo assembly of non-model organism's transcriptomes has recently been on the rise in concert with the number of de novo transcriptome assembly software programs. There is a knowledge gap as to what assembler software or k-mer strategy is best for construction of an optimal de novo assembly. Additionally, there is a lack of consensus on which evaluation metrics should be used to assess the quality of de novo transcriptome assemblies. RESULT: Six different assembly strategies were evaluated from four different assemblers. The Trinity assembly was used in its default 25 single k-mer value while Bridger, Oases, and SOAPdenovo-Trans were performed with multiple k-mer strategies. Bridger, Oases, and SOAPdenovo-Trans used a small multiple k-mer (SMK) strategy consisting of the k-mer lengths of 21, 25, 27, 29, 31, and 33. Additionally, Oases and SOAPdenovo-Trans were performed using a large multiple k-mer (LMK) strategy consisting of k-mer lengths of 25, 35, 45, 55, 65, 75, and 85. Eleven metrics were used to evaluate each assembly strategy including three genome related evaluation metrics (contig number, N50 length, Contigs >1 kb, reads) and eight transcriptome evaluation metrics (mapped back to transcripts (RMBT), number of full length transcripts, number of open reading frames, Detonate RSEM-EVAL score, and percent alignment to the southern platyfish, Amazon molly, BUSCO and CEGMA databases). The assembly strategy that performed the best, that is it was within the top three of each evaluation metric, was the Bridger assembly (10 of 11) followed by the Oases SMK assembly (8 of 11), the Oases LMK assembly (6 of 11), the Trinity assembly (4 of 11), the SOAP LMK assembly (4 of 11), and the SOAP SMK assembly (3 of 11). CONCLUSION: This study provides an in-depth multi k-mer strategy investigation concluding that the assembler itself had a greater impact than k-mer size regardless of the strategy employed. Additionally, the comprehensive performance transcriptome evaluation metrics utilized in this study identified the need for choosing metrics centered on user defined research goals. Based on the evaluation metrics performed, the Bridger assembly was able to construct the best assembly of the testis transcriptome in Fundulus heteroclitus.

Excitation-emission matrix scan analysis of raw fish oil from coastal New Jersey menhaden collected before and after Hurricane Sandy.

The impact of Hurricane Sandy (October 29, 2012) on PAH exposure was investigated in adult Atlantic menhaden (Brevoortia tyrannus) collected along the NJ coast. Collections were made in August, September and/or October of 2011, 2012 and 2013. PAHs were monitored in raw fish oil using excitation-emission matrix (EEM) spectroscopy. Results showed that raw fish oils had relatively high levels of high molecular weight, PAH-like compounds (173 to 24,421ng/mL) compared to values reported for bile in other species. EEM profiles resembled that of crude oil and excluded matrix interference by some common biological molecules that also fluoresce. Concentrations and EEM profiles varied by collection; however, collection ship, month, year and fish size did not account for the data. Replicates showed that fish from the same catch had similar PAH exposure. Overall, Hurricane Sandy did not alter body burdens of PAHs in raw fish oil of menhaden.

Detection of polycyclic aromatic hydrocarbons (PAHs) in raw menhaden fish oil using fluorescence spectroscopy: Method development.

Raw menhaden fish oil was developed for biomonitoring polycyclic aromatic hydrocarbons (PAHs) using fluorescence spectroscopy. Menhaden (Genus Brevoortia) were collected in 2010 and/or 2011 from Delaware Bay, New Jersey, USA; James River, Virginia, USA; Vermillion Bay, Louisiana, USA (VBLA); and Barataria Bay, Louisiana, USA (BBLA). Barataria Bay, Louisiana received heavy oiling from the Deepwater Horizon oil spill. Method development included determining optimal wavelengths for PAH detection, fish oil matrix interferences, and influence of solvent concentration on extraction. Results showed that some fish oils contained high molecular weight PAH-like compounds in addition to other fluorescent compounds such as albumin and vitamin A and vitamin E. None of these naturally occurring compounds interfered with detection of high molecular weight PAHs. However, data suggested that the lipid component of fish oil was altering fluorescence spectra by supporting the formation of PAH excimers. For example, the most intense excitation wavelength for hydroxypyrene shifted from Ex285/Em430 to Ex340/Em430. Comparison of Deepwater Horizon crude oil and fish oil spectra indicated that some fish oils contained crude oil-like PAHs. Using wavelengths of Ex360/Em430, fish oil concentrations were calculated as 3.92 µg/g, 0.61 µg/g, and 0.14 µg/g for a Delaware Bay sample, BBLA 2011, and VBLA 2011, respectively. Overall, these results supported using menhaden fish oil to track PAH exposures spatially and temporally.