Saturday, May 21, 2016
And now for something completely different....wait...now for something! Haven't had much time for hobbies lately, and now that I'm a little caught up I needed some inspiration and an email with the same title as this blog post did it!
The paper in that email is this gem from Y Maio et al., and is a combo- transcriptional and proteomics approach to understanding how scallops attach themselves to things. Here I've learned two things already. Scallops are attached to things! And I'm bad at counting.
Inside this paper I learn a couple more things rapidly. Scallops are ugly. Like super ugly and they have a lot of different components. Actually, it doesn't look too bad in this public domain image, but they are super ugly in the pic in the paper (and many of the other ones online).
The thing they want to study in this paper is the scallop attachment. And they do so by excising the scallop foot (that attaches these things to rocks and stuff) Unfortunately, they don't have a good genome for it, so its proteogenomics time...well, kinda...its time for transcriptomics and some peptide mapping! They use an Illumina platform for RNASeq during the attachment process and then cut gel-bands for MALDI-TOF and they do the relative protein quan by Coomassie staining.
I'm finding the genomics side of thing a little vague. It appears that they took their Hi-Seq output and then blasted the aligned output against everything that NCBI had for scallops and related organisms. This gave them 40,000 or so matches within their cutoffs and then they summed it up into GO. I'm guessing I missed something there, cause if they really did it that way there would be some serious sampling bias. I wouldn't be surprised if this is so intrinsic to translational analysis of this sort that its commonplace to glaze over this normalization.
What did this get them? For one, some new proteins, and some very strong suggestions that the few proteins that the scallop foot is composed of seem to have some serious PTMs that may be regulating the whole adherence process.
As I am trying to get my brain back into proteomics mode this was a nice paper to start out on. As a side note, I'd like to share one of the first images Google gives you when you look for a "Scallop Foot anatomy"