Comparing novel shotgun DNA sequencing and state-of-the-art proteomics approaches for authentication of fish species in mixed samples

Replacement of high-value fish species with cheaper varieties or mislabelling of food unfit for human con-sumption is a global problem violating both consumers' rights and safety. For distinguishing fish species in pure samples, DNA approaches are available; however, authentication and quantification of fish species in mixtures remains a challenge. In the present study, a novel high-throughput shotgun DNA sequencing approach applying masked reference libraries was developed and used for authentication and abundance calculations of fish species in mixed samples. Results demonstrate that the analytical protocol presented here can discriminate and predict relative abundances of different fish species in mixed samples with high accuracy. In addition to DNA analyses, shotgun proteomics tools based on direct spectra comparisons were employed on the same mixture. Similar to the DNA approach, the identification of individual fish species and the estimation of their respective relative abundances in a mixed sample also were feasible. Furthermore, the data obtained indicated that DNA sequencing using masked libraries predicted species-composition of the fish mixture with higher specificity, while at a taxonomic family level, relative abundances of the different species in the fish mixture were predicted with slightly higher accuracy using proteomics tools. Taken together, the results demonstrate that both DNA and protein-based approaches presented here can be used to efficiently tackle current challenges in feed and food authentication analyses.Proteomic

Benzo(a)pyrene reduces osteoclast and osteoblast activity in ex-vivo scales of zebrafish (Danio rerio [Hamilton-Buchanan, 1822]) and goldfish (Carassius auratus [Linnaeus, 1758])

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Expression of genes regulating protein metabolism in Atlantic cod (Gadus morhua L.) was altered when including high diet levels of plant proteins

Atlantic cod were fed five different diets consisting of a plant protein mixture replacing fishmeal in a regression design up to total replacement. Growth was high and maintained equal up to 75% plant protein inclusion, while a total plant protein diet resulted in significantly reduced appetite, feed conversion, and growth. To reveal if the transcription of stress responsive genes or any metabolic pathways were affected by plant proteins, a microarray consisting of 744 EST library-clones from cod was used on liver samples after the fish doubled its weight. Liver mRNA-expression of insulin-like growth factor II (IGF-II), insulin-like growth factor receptors I and II (IGF-IR, IGF-IIR), genes coding for proteolytic enzymes; cathepsinD (CatD), cathepsinF (CatF), calpain 2, and seven proteins involved in protein-biosynthesis and energy-turnover, were studied by means of quantitative real-time PCR. Transcriptional levels of IGF-IIR and CatD were reduced in the plant fed fish. With few exceptions, dietary inclusion of plant protein did not affect the expression of genes related to cellular stress, protein-biosynthesis or energy turnover when the fish was fed up to 75% plant protein inclusion. The data on down-regulation of the IGF receptors and CatD coincided with the reduced growth in the high plant inclusions, indicating that IGF and CatD responses were closely related to protein turnover. © 2010 Blackwell Publishing Ltd. No claim to original US government works