Sea stars, in my hands and on my computer

For the graph nerds out there: HIMYM Venn Diagram and HIMYM Charts and Graphs (both ~15 seconds). We should all make our pie charts with the units Percentage of Awesomeness.

Last night we dissected an evasterias and a pycnopodia. Mo generously brought us a small pycnopodia from South Shaw, where she had been diving that day. It wasn’t lesioned, but Mo said it was starting to curl its many arms in unnatural directions. We took coelomic fluid, tube feet, nerve tissue, caecum, and dermis. Despite being much softer than the many pisaster we had on Friday, in several ways the pycnopodia was more difficult to work with because of its lack of stiffness. Its sliminess made it difficult to get a good grip, and the poor sea star was so stressed that it kept dropping its arms whenever I went to get any tissue. I haven’t worked with pycnopodia before, but I think that they drop limbs much more readily than pisaster, both because they have so many and because their tissues are easy to break through. Even though it was a sign of stress that the pycnopodia was dropping arms, it was still fascinating to observe the central disk as it happened. The break was always clean and at the same place, just above the start of the digestive caecum. Within a minute, you would never guess there had been an arm there to begin with (unless they lost several right next to each other), since they pull in the opening to minimize fluid loss.

We continued our investigation of the pycnopodia transcriptome with a combination of iPython, R, and David. The site David allows comparisons of gene expression in a treatment sample compared to a reference sample. We used stars injected with homogenate of wasting pycnopodia as our treatment, and used stars injected with heat-killed homogenate as our reference (background). The genes that showed differential expression in the treatment group were involved with immune response, among other things. While it may seem obvious, sometimes obvious results are a good thing, and they tell you things that make sense. If no immune system processes changed in the treatment stars, it might suggest that we did something wrong, or that the pathogen was not triggering an immune response (which was clearly not the case with the visible lesions, but immune response not a given in every organism or every disease, depending on how well the pathogen can avoid detection while causing damage). So, the sea stars are changing the expression of genes under the major category of immune response. Today we just looked into biological processes, but as we get down to more specific cellular components or molecular functions, perhaps the genes with differential expression can tell us something about the nature of the pathogen. This will be helpful, since so far the histology has not shown many differences in the tissues of wasting and healthy animals, aside from general epithelial decay.

Here’s a breakdown of the biological processes that get upregulated or downregulated during sea star wasting in pycnopodia. In the left panel, the processes are arranged by overall similarity, with color noting significance level. In the right panel, the processes are grouped by color, and general size of the square represents the number of genes involved in the process. I think this is a great way to quickly visualize what processes are most important, and more quantitative visuals can come later if needed.

revigo semantic space Revigo Differentially expressed genes

Here is my notebook from today.

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