Project description:Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.
Project description:Seafood fraud has become a global emerging issue, threatening food security and safety. Adulteration, substitution, dilution, and incorrect labeling of seafood products are fraudulent practices that violate consumer safety. In this context, developing sensitive, robust, and high-throughput molecular tools for food and feed authentication is becoming crucial for regulatory purposes. Analytical approaches such as proteomics mass spectrometry have shown promise in detecting incorrectly labeled products. For the application of these tools, genome information is crucial, but currently, for marine species of commercial importance, such information is unavailable. However, when combining proteomic analysis with spectra library matching, commercially important fish species were successfully identified, differentiated, and quantified in pure muscle samples and mixtures, even when genome information was scarce. This study further tested the previously developed proteomic-based spectra library-based approach was further tested to differentiate 29 fish species from the North Sea in individual samples, laboratory-prepared mixtures, and commercial samples. For authenticating libraries generated from 29 fish species, fresh muscle samples from the fish samples were matched against the reference libraries. Species of the fresh fish samples were correctly authenticated using the spectra libraries generated from the 29 fish species. Furthermore, processed commercial products containing mixtures of two or three fish species were matched against these spectra libraries to test the accuracy and robustness of this method for authentication of fish species. The results indicated that the method is suitable for the authentication of fish species from highly processed samples such as fish cakes and burgers. Spectra libraries built from 29 fish species in the North Sea can efficiently tackle current and future challenges in feed and food authentication analyses when prospecting new resources in the Arctic.
Project description:Transcriptional responses to hypoxia were compared between a hypoxia tolerant fish (tidepool sculpin; Oligocottus maculosus) and a hypoxia intolerant fish (silverspotted sculpin; Blepsias cirrhosus). To determine if, and how, transcriptional plasticity is associated with differences in hypoxia tolerance, each species was subjected to a hypoxic time-course and liver was sampled at normoxia, 3hr, 8hr, 24hr, 48hr and 72hr of hypoxia. The hypoxic level for each species was scaled to the species' own tolerance level (relative exposure) in order to elicit similar tissue level hypoxia between the two sculpin species. Each species was also subjected to a single environmental O2 tension (absolute exposure) and sampled at 24 hrs of hypoxia.
Project description:Replacement of high-value fish species with cheaper varieties or mislabelling of food unfit for human consumption 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.
Project description:The goal of this study was to measure the effect of heat stress on the transcriptome of a cold-adapted fish species - Trematomus bernacchii - an Antarctic fish species. Keywords: Stress response