Wednesday, February 27, 2008

Jennifer Successfully Defended Her Thesis Today

Jennifer's thesis defense went well this afternoon. She started out a little awkwardly, but once she got past her second sentence she kicked into gear and spoke well; I've seen severe stage fright at these events in the past, and luckily she shook it off quickly. In the post-defense meeting with the full thesis committee (four members, plus an outside observer from Computer Science representing the Graduate Studies dean) we kicked around some ideas to make her thesis stronger. This was good, since I realize that I've been too close to this project and I'm grateful to Profs. Lawton and Wang (the latter from A&M) for their constructive criticisms for ways to improve the presentation of the work. This is especially useful for coming up with a version of the work for submission to a journal. So, once Jennifer incorporates these suggestions into her work she has fully completed the requirements for her Masters.

Next Wednesday Enrique defends his thesis, which focuses on differences in brain structure between male and female scarlet shiners. This will also be at 2 p.m., in room 107 in the Shelby Center.

Saturday, February 23, 2008

We Now Have Hillabee Creek F. bifax DNA, Too

Andrew and James were able to get very strong DNA extractions from four stippled studfish we collected in Hillabee Creek. These concentrations are around 300 nanograms/microliters with absorbance ratios of about 1.9. I think our next project will be some extractions from northern or southern studfish for comparative purposes. Next Saturday we make a return trip to Tallapoosa County to hit some other sites and see if we can find stippleds. The weather forecast is good, over 60 F. and sunny. I hope so!

Jennifer defends her thesis on Wednesday, entitled


If you're in Huntsville this Wednesday, it's at 2 p.m. in room 301 of the Shelby Center. Hope to see you there.

Tuesday, February 19, 2008

It's For Real, We Have Quality Stippled Studfish DNA

I was able to test the concentration and general quality of our stippled studfish DNA yesterday with Andrew. We were able to use the NanoDrop spectrophotometer in the Podila lab, which can assay 1.2 microliters of your product and give you a computer screen of information. Our four extractions from stippled studfish (Fundulus bifax) from Cornhouse Creek in Randolph County, AL, varied in concentration from 103 - 220 nanograms/microliter of DNA, with the 260/280 nm wavelength ratios indicating DNA/protein ratios varying between 1.83 - 2.2. The higher end of the ratios may reflect light phenol contamination since phenol absorbs well at a wavelength of 260 nm, but probably nothing to worry about for PCR purposes. We also had similar good results with our initial test extraction done on a F. similis from Dauphin Island, AL. So we're in business.

Hopefully we'll get out tomorrow to collect more scarlet shiners at Limestone Creek as part of our monthly assessments of growth. The weather will be in the mid 50's F, with some chance of rain.

Wednesday, February 13, 2008

Praise Jah, We Can Extract Fish DNA

I did a test DNA extraction today with James and Andrew. We did it the way described in Kocher et al. (1989), with PCI/CI phase extractions to concentrate DNA in an aqueous phase and strip out proteins on top of hydrophobic phases. It worked because Joe Leahy was kind enough to let me use some of his unopened PCI, since mine apparently went bad over a year ago. So we used a Fundulus similis (longnose killifish) from a Dauphin Island collection as a test subject, slicing off some white muscle for tissue. It worked great, we got a nice little grayish/whitish smear for a pellet after the frozen ethanol precipitation. We'll test its concentration and purity on Friday using Joe's UV spectrophotometer. If that gives us good numbers we'll go ahead and extract DNA from F. bifax I collected at Cornhouse Creek in Randolph county with Joe Scanlan a few years ago. I've pretty much decided to go ahead with this method of DNA extraction rather than the kits, because it yields a fair amount of DNA suspended in TE buffer for PCR reactions. Alright, we're gene jockeys! (At least we collect our own fish...)

Friday, February 08, 2008

Good News From Birmingham Audubon

I've learned that I've won a research grant from the Walter F. Coxe Fund of Birmingham Audubon. They decided to fund most of my proposal to study the distribution status and population structure of the stippled studfish, Fundulus bifax. This is a huge relief, and I'm grateful to the review committee for seeing merit in my proposal. Now I have the financial resources to pull off all of the lab work: extracting DNA, amplifying the DNA via PCR and sequencing the PCR product. I hope to do the next field trip to Tallapoosa county on Saturday, March 1, weather permitting.

Also, be on the look out for a new NANFA t-shirt. Casper Cox is designing one that'll have a full color rainbow darter on the front. I mean, how often do you come across a high quality t-shirt with a rainbow darter on it?!? It will cost $20, plus $5 shipping, and will hopefully be available in the next month or two.

Tuesday, February 05, 2008

Correction For The Lythrurus Shiner In Hillabee Creek

In my last post I mentioned that I thought we had found ribbon shiners in Hillabee Creek. I suspected that was a very loose ID, and now I realize that what we found were actually pretty shiners, Lythrurus bellus. This is what happens when I get outside of the Tennessee drainage, and down into the Mobile drainage. I also corrected another mis-identification; the one darter that we found in Hillabee Creek I called blueside, when of course it was a speckled. Both have blue blotches on the side, but the speckleds have more of a turquoise color. Again, this was going on autopilot for Tennessee vs. Mobile drainage. If I was up in Sipsey Fork, I would have immediately said speckled, but that didn't happen over in the Tallapoosa drainage. Oh well...

And I hope everyone's having a good Mardi Gras, and voted for whom I voted.

Monday, February 04, 2008

Scarlet Shiner Size Distributions, And We Made It To Tallapoosa County

First order of business, we have a surprisingly good graph of size distributions of the scarlet shiners we caught at Limestone Creek and Estill Fork. I broke these down as increments of 5 mm in length. For our large data set from Limestone Creek, you can see evidence of three year-classes of fish: those born last summer are 20-40 mm long, those now in their second year are 40-60 mm long, and those in their third year are longer than 60 mm long. The much smaller sample from Estill Fork is also on this graph, seemingly slightly larger on average than the Limestone Creek young-of-the-year. This is useful to us because it supports the idea that the adult scarlets we've been working with are mostly third-year fish, >60 mm long. I wasn't sure before whether or not breeding adults were all third year fish, or also a fair number of second year fish.
In other news, we made our first run to Coosa and Tallapoosa counties in central Alabama looking for the stippled studfish, Fundulus bifax. And even better, we found some. Unfortunately I forgot my camera so I don't have any pictures. But we caught a single studfish at the first creek we stopped at, Elkahatchee Creek in Coosa County. The water was turbird and a little high; we may stop there again in the future. We also stopped at another nearby branch of Elkahatchee Creek, where James must have tossed his cast net about 70 times without catching a single fish of any kind. So, we headed off to Hillabee Creek in Tallapoosa County, on State Route 22 near Alexander City. Hillabee turns out to be this wide, beautiful creek full of fast riffles flowing over step formations of sandstone(?) upstream of the bridge. After bringing the truck down the muddy clay access road from the highway we were able to wade out and deploy our seine on the edge of flowing runs. In just over an hour we caught 6 stippled studfish. I have a suspicion that the Hillabee Creek system is a stronghold of stippled studfish, as it's a good sized stream draining much of the county. We also caught a surprising number of small shadow bass, and lots of Tallapoosa shiners and ribbon(?) shiners (the latter a Lythrurus species for sure). With four people along this was fairly easy, so thanks to James, Andrew and Kayley(?) for going on this all-day venture.

The only odd part of the day was finding a recently executed yellow dog laid out on a low hummock along the creek, with a single gunshot through the head. Another dead dog was also further up under the bridge. If anyone has any insights on the attraction of executing your dog under a highway bridge along a creek and leaving the body, please tell me. This is a weird Southern thing that drives me crazy. I can understand wanting to do a quick, cheap euthanasia. But why leave the dog's body behind to rot in an otherwide beautiful creek? My cynical thought is to use this as a measure of whitetrash influence in an area. But that's probably way too simple.