Proteomic profiling of sea bass muscle by two-dimensional gel electrophoresis and tandem mass spectrometry

Molecular Rapid Test for Identification of Tuna Species

Tuna is an excellent food product, relatively low in calories, that is recommended for a balanced diet. The continuously increasing demand, especially for bluefin-tuna-based food preparations, and its relatively high market price make adulteration by intentionally mixing with other lower-priced tunas more prospective. The development of rapid methods to detect tuna adulteration is a great challenge in food analytical science. We have thus developed a simple, fast, and low-cost molecular rapid test for the visual detection of tuna adulteration. It is the first sensor developed for tuna authenticity testing. The three species studied were Thunnus thynnus (BFT), Thunnus albacares, and Katsuwonus pelamis. DNA was isolated from fresh and heat-treated cooked fish samples followed by PCR. The PCR products were hybridized (10 min) to specific probes and applied to the rapid sensing device. The signal was observed visually in 10-15 min using gold nanoparticle reporters. The method was evaluated employing binary mixtures of PCR products from fresh tissues and mixtures of DNA isolates from heat-treated tissues (canned products) at adulteration percentages of 1-100%. The results showed that the method was reproducible and specific for each tuna species. As low as 1% of tuna adulteration was detected with the naked eye.

Liver proteomics of gilthead sea bream (Sparus aurata) exposed to cold stress

The gilthead sea bream (Sparus aurata, L.) is very sensitive to low temperatures, which induce fasting and reduced growth performances. There is a strong interest in understanding the impact of cold on fish metabolism to foster the development and optimization of specific aquaculture practices for the winter period. In this study, an 8 week feeding trial was carried out on gilthead sea bream juveniles reared in a Recirculated Aquaculture System (RAS) by applying a temperature ramp in two phases of four weeks each: a cooling phase from 18 °C to 11 °C and a cold maintenance phase at 11 °C. Liver protein profiles were evaluated with a shotgun proteomics workflow based on filter-aided sample preparation (FASP) and liquid chromatography-mass spectrometry (LC-ESI-Q-TOF MS/MS) followed by label-free differential analysis. Along the whole trial, sea breams underwent several changes in liver protein abundance. These occurred mostly during the cooling phase when catabolic processes were mainly observed, including protein and lipid degradation, together with a reduction in protein synthesis and amino acid metabolism. A decrease in protein mediators of oxidative stress protection was also seen. Liver protein profiles changed less during cold maintenance, but pathways such as the methionine cycle and sugar metabolism were significantly affected. These results provide novel insights on the dynamics and extent of the metabolic shift occurring in sea bream liver with decreasing water temperature, supporting future studies on temperature-adapted feed formulations. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD011059.

Overview on Untargeted Methods to Combat Food Frauds: A Focus on Fishery Products

Authenticity and traceability of food products are of primary importance at all levels of the production process, from raw materials to finished products. Authentication is also a key aspect for accurate labeling of food, which is required to help consumers in selecting appropriate types of food products. With the aim of guaranteeing the authenticity of foods, various methodological approaches have been devised over the past years, mainly based on either targeted or untargeted analyses. In this review, a brief overview of current analytical methods tailored to authenticity studies, with special regard to fishery products, is provided. Focus is placed on untargeted methods that are attracting the interest of the analytical community thanks to their rapidity and high throughput; such methods enable a fast collection of “fingerprinting signals” referred to each authentic food, subsequently stored into large database for the construction of specific information repositories. In the present case, methods capable of detecting fish adulteration/substitution and involving sensory, physicochemical, DNA-based, chromatographic, and spectroscopic measurements, combined with chemometric tools, are illustrated and commented on.

Comparative proteomic analysis of two clam species: Chamelea gallina and Tapes philippinarum

Clams have long been a fisheries and aquaculture sector of great importance in Italy, the main resource of fisheries is the Chamelea gallina of indigenous origin, whereas clams breeding is supported almost entirely by the Tapes philippinarum, a species of Indo-Pacific origin. Bivalve molluscs quality depends mainly on the water quality, and then by a series of factors such as water temperature and salinity, gametogenic cycle, food availability, and environmental conditions, that affect the Condition Index. In this work crude extracts obtained from the edible part of Chamelea gallina and Tapes philippinarum were analyzed by a proteomic approach based on a two-dimensional gel electrophoresis followed by liquid chromatography-tandem mass spectrometry, in order to detect biomarkers useful for identification of the two kinds of clams and to assess their nutritional characteristics. As a result, four differentially expressed spots were found and identified, namely enolase, cyclophilin-A, ribosomal protein L13 and actin-1.

Proteomic profiling of white muscle from freshwater catfish Rita rita

Muscle tissues contribute 34-48 % of the total body mass in fish. Proteomic analysis enables better understanding of the skeletal muscle physiology and metabolism. A proteome map reflects the general fingerprinting of the fish species and has the potential to identify novel proteins which could serve as biomarkers for many aspects of aquaculture including fish physiology and growth, flesh quality, food safety and aquatic environmental monitoring. The freshwater catfish Rita rita of the family Bagridae inhabiting the tropical rivers and estuaries is an important food fish with high nutritive value and is also considered a species of choice in riverine pollution monitoring. Omics information that could enhance utility of this species in molecular research is meager. Therefore, in the present study, proteomic analysis of Rita rita muscle has been carried out and functional genomics data have been generated. A reference muscle proteome has been developed, and 23 protein spots, representing 18 proteins, have been identified by MALDI-TOF/TOF-MS and LC-MS/MS. Besides, transcript information on a battery of heat shock proteins (Hsps) has been generated. The functional genomics information generated could act as the baseline data for further molecular research on this species.

Differentiation between fresh and frozen-thawed sea bass (Dicentrarchus labrax) fillets using two-dimensional gel electrophoresis

This study aimed to identify a protein marker that can differentiate between fresh skinless and frozen-thawed sea bass (Dicentrarchus labrax) fillets using the two-dimensional polyacrylamide gel electrophoresis (2-DE) technique. Distinct gel patterns, due to proteins with low molecular weight and low isoelectric points, distinguished fresh fillets from frozen-thawed ones. Frozen-thawed fillets showed two specific protein spots as early as the first day of the study. However, these spots were not observed in fresh fillets until at least 13days of storage between 0 and 4°C, fillets were judged, beyond this period, fish were unfit for human consumption as revealed by complementary studies on fish spoilage indicators namely total volatile basic nitrogen and biogenic amines. Mass spectrometry identified the specific proteins as parvalbumin isoforms. Parvalbumins may thus be useful markers of differentiation between fresh and frozen-thawed sea bass fillets.

Impact of three commercial feed formulations on farmed gilthead sea bream (Sparus aurata, L.) metabolism as inferred from liver and blood serum proteomics

Background

The zootechnical performance of three different commercial feeds and their impact on liver and serum proteins of gilthead sea bream (Sparus aurata, L.) were assessed in a 12 week feeding trial. The three feeds, named A, B, and C, were subjected to lipid and protein characterization by gas chromatography (GC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively.

Results

Feed B was higher in fish-derived lipids and proteins, while feeds C and A were higher in vegetable components, although the largest proportion of feed C proteins was represented by pig hemoglobin. According to biometric measurements, the feeds had significantly different impacts on fish growth, producing a higher average weight gain and a lower liver somatic index in feed B over feeds A and C, respectively. 2D DIGE/MS analysis of liver tissue and Ingenuity pathways analysis (IPA) highlighted differential changes in proteins involved in key metabolic pathways of liver, spanning carbohydrate, lipid, protein, and oxidative metabolism. In addition, serum proteomics revealed interesting changes in apolipoproteins, transferrin, warm temperature acclimation-related 65 kDa protein (Wap65), fibrinogen, F-type lectin, and alpha-1-antitrypsin.

Conclusions

This study highlights the contribution of proteomics for understanding and improving the metabolic compatibility of feeds for marine aquaculture, and opens new perspectives for its monitoring with serological tests.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-014-0044-3) contains supplementary material, which is available to authorized users.