Science is all crap.
Well, it has been a few days and I have no new data. I forgot what this was like: as a postdoc, stuff has generally worked for me. I've had some dry spells, but I usually always have something cooking. A few days of solid failure brings me back to grad school... ahh, grad school. What a miserable time that was!
What I can report is that I can't clone this mystery protein, now that I know what it supposedly is. I can detect the transcript, no problem, using a commercial quantitative PCR kit (of course the sequences of their probes are proprietary). But when I go to amplify it to clone it, nada. Nothing. So I don't know if the Q-PCR is crap (probably) or if it's all my fault (quite possibly). Probably both!
Meanwhile, I have been trying to do sequence alignments. Now mind you, I'm familiar with proteins that are not well-conserved, and I have done quite a few alignments using CLUSTALW, and by hand. So my mystery protein is supposedly related to a well-conserved family of proteins, and it comes up in BLAST with this similarity. But when I do alignments with various family members, it is not at all obvious that this protein actually belongs to this family. Depending on which member I choose, I get a totally different alignment. I mean, TOTALLY. If there are really 20 conserved residues, as the literature says, in this family, shouldn't those at least come up every time? Noooooo....
Anyway I guess I am off to prep more RNA, because I'm worried my cells might not last until tomorrow if I blow it off, and possibly stain some coverslips, mostly because I'm worried I will be too lazy to come in and do it tomorrow.
Hard to want to come in for more punishment on the weekend.