Use of ‘omics’ to identify molecular markers of livers affected by exposure to toxic cyanobacteria in salmon
Cyanobacteria, commonly called blue-green algae, can produce microcystins which are well recognized as extremely potent hepatotoxins that are associated with changes in gene expression, physiology and morphology in numerous animals, including fishes. Microcystins (MC) are commonly found in freshwater but also present in marine environments where they are linked to the development of a severe liver disease called net-pen liver disease (NPLD) in farmed and wild Atlantic and Chinook Salmon, which is characterized by hepatic lesions that include megalocytosis and loss of gross liver structure. In British Columbia (BC) Canada, NPLD is costs the BC salmon farming industry tens of millions of lost revenue annually.
The link between acute MC exposure and NPLD was recently investigated and it was found that although acute MC exposure does not produce the characteristic lesions associated with NPLD, there are severe but reversible changes in hepatic structure (Shartau et al., submitted; Journal of Fish Disease) and gene expression (Shartau et al., unpublished).
The rapid change in gene expression in response to MC exposure suggests that gene markers may be useful for monitoring toxin exposure and ultimately allow farm managers to reduce the impact of harmful algal blooms and gauge effectiveness of their mitigation efforts. These measurable changes in response to toxin exposure can be used as biomarkers to assess exposure to environmental toxins. Biomarkers for MC and domoic acid (another algal toxin) exposure have been identified in whitefish and zebrafish, respectively, and in Atlantic salmon in response to metal toxicity. The ability to use biomarkers is a valuable tool in the management of ecosystem quality, acting as an early warning system preceding more severe toxic events involving fish morbidity and mortality. To examine candidate biomarkers in Atlantic and Chinook Salmon, we selected liver samples from our previous exposure trial and submitted these for RNA-sequencing.
We have recently received the sequencing data for these samples and now seek a graduate student to complete the following objectives as the central part of a MS degree:
1) Align sequences to a reference genome
2) Estimate gene- and transcript-level abundances
3) Perform differential expression analysis
4) Visualize and summarize the output of RNA-seq analysis
5) Write up the results for submission to a peer-reviewed journal
In addition to the above, the student will have the opportunity to ask their own questions related to this data set, and to participate in other research projects in the lab in the area of environmental physiology and toxicology.
Applicants must have a Bachelor’s degree relevant to biology, should have a strong academic background and possess excellent written and oral communication skills in English. The student must possess a keen interest and an aptitude for bioinformatics, and excellent computer skills including experience with linux operating systems. This includes prior bioinformatics experience and/or completion of bioinformatics courses. The student should also have an interest in animal physiology.
Twelve months of salary and partial tuition support will be provided for up to 2 years through a combination of research and teaching funding, pending satisfactory performance. For further information or if you wish to pursue this opportunity, please contact Dr. Ryan Shartau (firstname.lastname@example.org).
If you want to apply for this opportunity, please provide the following:
1) 1-2 paragraph statement on your motivation and qualifications,
2) Unofficial transcript,
4) Names and contact information for 3 references
Applications will be considered starting January 31st, 2022 and be considered until the position is filled. Start date will be September 2022 but a summer start date can be negotiated.