Winter Blahs, So Let's Go Fool With Some Fish

I'm entering the phase in my Vertebrate Zoology class where I blitzkrieg through ancestral and modern fishes as examples of the base of vertebrate diversity. Does the phrase Meckel's cartilage ring a bell with you? Do you count gill slits in fish illustrations to check for anatomical accuracy? I sincerely hope that you answered yes to both.

Yesterday I tried to extract DNA from fish for the first time in 2 years. We could use some new mtDNA sequences for the mummichog population structure study, and the longnose/striped killifish study, so I'm training an undergraduate in extraction and hopefully also in PCR. I pulled out four longnoses from St. Joe Beach in Florida for a demonstration of the technique, since these are large fish easy to cut off white muscle strips for extraction. It went great at first; but I screwed up the extractions by somehow emulsifying the protein purification stage where hydrophilic and hydrophobic phases are used to separate out undesirable proteins. Instead of two layers in the tubes, we just had uniform murky fluid. Damn! The last time I did that was 3 years ago when I first showed Brace how to do this. I think we added too much tissue to each extraction tube. Next time, next week, we'll use just half as much. But it was fun to do some real biology work again.

Where this is all going is to come up with some more mtDNA cyt-b sequences for Kris' work. We don't have quite enough sequences from northern populations of Fundulus heteroclitus to really ice our analysis. I realize that I have some Queens, NY fish (!) that I never used so I'd like to get them sequenced. And even worse, when we had our first batch of PCR amplification products sequenced by a commercial service they screwed up many of our sequences. At first one of their employees told us to purify the DNA in one fashion, and just as we sent them our purified samples another employee basically told us that he couldn't believe we were so stupid as to do it that way. Well, at least some of the sequences came back in usable form. So I've found another vendor who is willing to do the work for $7/sample rather than a flat rate of $256 for 96 samples like the original vendor. Since I want to run no more than 10 sequences, paying for it myself, this is a good deal I hope. And this all made possible by my discovery of an unused tube of Taq polymerase in my freezer, so we won't have to shell out the $50 for more.

On Monday afternoon I hope to get out to Limestone Creek to collect black darters to send to Thomas Near at Yale for genetic analysis. At least two students are willing to go with me for this. The forecast is for a high temperature of 49 deg. F that day which will hopefully be tolerable. I have three sets of insulated waders, so we should be set. I'm in need of a collecting trip, even falling in the creek could be fun!