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Title: Understanding the molecular basis of dietary protection against sea lice in Atlantic salmon : application of proteomics and transcriptomics
Author: Micallef, Giulia
Awarding Body: University of Aberdeen
Current Institution: University of Aberdeen
Date of Award: 2013
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Yeast cell wall (YCW) extracts have long been regarded as beneficial supplements in aquaculture feeds, especially with respect to immunomodulation. Previous studies have shown that supplementing salmon diets with YCW extracts increases resistance to sea lice. During the series of three trials, different sea lice challenge models and YCW extracts were studied. In Trial 1, fish fed a diet containing 0.4% YCW #a exhibited a significant reduction in sea lice burden of 23% compared to the control diet. The skin and skin mucus samples from Trial 1 were hence used for high-throughput screening of altered transcripts and proteins, while searching for candidate biomarkers for YCW extracts. Samples from Trials 2 and 3 were used for testing the candidate transcripts in independent biological samples, hence confirming or otherwise their suitability as biomarkers. Due to the lack of skin-specific libraries in the salmonid EST database, Roche-454 sequencing was used to describe the skin transcriptome of Atlantic salmon and form the basis of successive experiments. The resulting transcriptome assembly included 4,108 transcripts that were previously unknown for salmon, which include both skin-specific and low-expression transcripts. Analysis of the mucus proteome by 2D gels of Trials 1 and 2 samples showed that 27 and 49 proteins, respectively, exhibited a change in expression due to dietary treatment (p<0.05). Of these, calreticulin-like protein showed greatest potential as a biomarker since its expression was changed in both Trials 1 and 2 at the proteomic level and Trials 2 and 3 at the transcriptomic level. RNAseq was carried out on Trial 1 skin samples and 375 transcripts were significantly altered in expression across dietary treatments (p<0.05). Validation of this data by qPCR was successful and yielded similar fold changes to the RNAseq output. However, when the expression of a selection of genes was studied in Trial 2 samples, no correlation was found and hence, no candidate biomarker molecules were discovered. While further work is required to deduce the underlying mechanisms of immunomodulation due to dietary YCW extracts, this project has yielded two skin-specific transcriptomic databases which may be used to enhance the genomic data for salmonids.
Supervisor: Not available Sponsor: BioMar
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Atlantic salmon