Monday, April 28, 2008

Stuck In The Mud... Really

Above is a photograph of a male stippled studfish from upper Hillabee Creek in Tallapoosa County, AL. It's not the best picture, but I hope you get the idea, especially the "stippling" of red-brown spots in random line patterns on the side. For scale you can see Andrew's thumbnail in the lower left corner, holding up his wading boot with the fish on it.

We went back to the area on Saturday and visited three historic stippled studfish (Fundulus bifax) sites. Joe Scanlan met us at Elkahatchee Creek and this time we caught and kept 7 studfish. Talking with him I realize there's a very simple pattern to finding creeks with stippled studfish: they have to have clear water, not be even slightly eutrophic, and there has to be extensive areas of sand and fine gravel as substrate. This describes all three creeks we visited on Saturday, and we found bifax at all three sites.

At the second site, in the NW corner of Tallapoosa County, I got the truck stuck in mud. There was a dirt road off of the paved road heading down to the creek, and it looked passable with one major rut area about halfway down. I put the truck in 4WD and drove into the rutted area; boom, we were instantly stuck in what Andrew and James described as a wall of mud. We spent an hour pushing the truck, putting rocks and wood under the wheels, all to no avail, it was stuck up to the front axles in mud. James and I walked up to a house we could see, but no one was home. A car came down the highway, I stuck out my thumb (no cell phone coverage) and the car slowed down, turned around, and stopped by us. The driver was a farmer from the other direction. He said, "That must be you stuck down there, it happens all the time. I'll be back in a minute." And luckily he was, driving a tractor. We connected a chain to the rear of the truck, and the tractor pulled the truck right out of the mud. God, we were lucky; I have no idea how we would have gotten out otherwise. Afterwards, I drove the truck closer to the highway. We went into the creek which was good just to wash off the mud. And, we caught 8 bifax, in slow-moving water over sand and gravel upstream of a sandbar.

Amazingly we still had time for one more stop, so we headed north into a maze of unpaved county roads looking for a tributary to Hillabee Creek. The place we wanted was blocked off by a locked gate and No Trespassing sign. My best map showed a road from that crossroads crossing a smaller unnamed creek to our west, so we drove west and soon found the site pictured below. The water was very clear, with some flat rocks installed in the ford you see below for traction over the (yes, you guessed it) sand and fine gravel substrate. We almost immediately netted bifax from the stream, just to the left of this picture's view.
With that, we headed home, throwing mud from the undercarriage almost all the way to Birmingham. Yesterday I spent about an hour hosing mud and sand from the undercarriage of the truck. And I still feel very lucky.

Wednesday, April 23, 2008

Shock & Awe In Alabama

Not explosives, but it's the result of out-of-staters collecting fish in Lick Fork of the Paint Rock River yesterday. Tom from Connecticut and friends from California spent the day netting in Lick Fork at my recommendation, and they're in shock from the numbers of fishes, the species diversity, and the size of various fishes in a fairly small stream. I keep telling anyone who will listen that here in the Tennessee Valley we're at ground zero for North American biodiversity, and Tom and his pals will testify to that. We tend to take it for granted around here. But I spent 20 years in Boston, and I know that the diversity is way lower (except for the ocean...). They'll join us today on our last scarlet shiner trip of the year to Limestone Creek. Daniel and Sandi are both graduating, so I'll have to figure out how to keep this size monitoring project going over the summer.

Monday, April 21, 2008

It Took Most Of The Day, But...

...I finally have access to my grant money. This means I'm on the university's finances & budget management website, the BANNER system. The people who manage various parts of the system are very nice, I just needed a more or less free day to walk around and talk to them. That's the modern American university; in my more cynical moments I try to come to grips with the reality that the beancounters have taken over. Now I can stop leeching off of other labs for material like ethidium bromide.

This Saturday we head back to the Tallapoosa. I think we'll go back to Elkahatchee Creek in Coosa County and see if we can find more stippled studfish. In February we caught one there, and I suspect that we can find more. If that goes well we'll hit some scattered sites in Tallapoosa County, and we should be about done with Tallapoosa County. That'll leave three sites in Elmore County to the south, and then I'll shift to surveying unexplored creeks in Cleburne County to the northeast. And, of course, we'll be doing DNA work in the lab, like all good gene jockeys do.

Friday, April 18, 2008

And Yet More Successful Bifax DNA PCR Runs

From our latest batch of 7 stippled studfish DNA extractions, 3 showed amplification bands. So now we have amplified DNA from 4 individuals from Hillabee Creek, and 1 from Cornhouse Creek. Another set of 7 fish went through the thermocycler today, so hopefully on Monday we'll run the gels and see if the PCR worked. Three of these fish are southern studfish, three are northern studfish, and one is a pretty shiner that we kept and extracted just to see what happens. A success rate of five of thirteen isn't bad for working with hodgepodge reagents.

I finally brought over the last two fish from the giant aquarium back at Wilson Hall. These two blackspotted topminnows are now in the new 20-gallon tank in my lab. They were eating flake within five minutes. The giant tank itself will probably be moved over here to the Shelby Center and set up as a public display tank in the front lobby by a coalition of the Biology and Chemistry Clubs. Anything they do will be good; the Dean has tentatively approved the idea. I think he'll like it!

Thursday, April 17, 2008

I Went Out To See The Flint River, And More Bifax PCR

I went out yesterday to look at a stretch of the Flint River to put together a quote for a faunal survey. The local water treatment system needs more outfalls, since the suburbs have overrun former farm land. I don't approve, really, but I guess it beats people not having sewage treatment(!). The river was high and fast, with a good 15 knot current. It would not have been a good day either to seine fish, or to dive for mussels. It was still a beautiful day, on what is still a largely unspoiled river, and for "lunch" I got to 4-wheel around pastures and fields to get to the site. The only listed fishes in the river by Fish & Wildlife standards are the slackwater darter and the snail darter, both Threatened. But the slackwater is found only much further upstream, and the snail has never been collected from the Flint although it has been found in the Paint Rock just to the east. We'll see...

James & Andrew started another PCR attempt yesterday with DNA samples from stippled studfish from Hillabee Creek in Tallapoosa County and Cornhouse Creek in Randolph County. They used the optimal thermocycler program (so I think). They'll run a gel tomorrow and see if we have more successful product for sequencing. And, I'll finally sit down with Terence from Procurement on Monday to get my grant account activated. Money doesn't talk, it swears.

Saturday, April 12, 2008

The First Successful PCRs Are Hillabee Creek Bifax

I just heard from James (thanks, James!) that the two Fundulus bifax DNA extractions that were successfully amplified were from Hillabee Creek in Tallapoosa County, AL. These extractions are both high quality, so I'm not surprised. This week I hope we can re-run the four that didn't amplify using a better temperature program in the thermocycler, and toss in a few others too. And maybe by the end of the week I'll finally have access to my grant money...

Friday, April 11, 2008

PCR Success With Bifax DNA

Kris, Andrew and James did the first PCR runs on our extracted Fundulus bifax DNA over the past two days. Out of six samples they ran, two produced bands as evidence of amplification which is a good first start. They ran a slightly wrong program on the thermocycler with shorter extension times than works best, so I'm happy that two of six actually worked. So we're in gear. I also hope to get access to my research funds soon; I went to a training program yesterday morning that fizzled because the university computer system was down, and the training software was unavailable. The trainer, who works in University Procurement, graciously told me he'd give me a tutorial on it since he knows I only need a small part of their overall training. With my own money available we can avoid embarrassing things like borrowing 5 microliters of DNA ladder from another lab who asked Kris to sign it out in their chemical logbook. We should probably just give them a dollar and be done with it, but who am I to say.

I've started to set up a 55-gallon tank in my lab. It fits nicely with the 20-gallon already there. I hope to have fish in both sometime soon...

Monday, April 07, 2008

PCR Of Stippled Studfish DNA On Wednesday, I Hope

Wednesday morning I hope to start the first PCR run of extract stippled studfish DNA. From what I can tell I've found everything that we need, for the first run since I moved in to the new lab. I won't be able to order anything off of my grant money until at least Thursday, so we'll do it with some Taq polymerase I've had for a year in the freezer. If it works, great, if not, we'll at least have gone through a dress rehearsal.

Ruth and I went out to Borden Creek in the Sipsey Wilderness yesterday. The creek was high and flowing fast, I'm glad we weren't trying to net fish because it would've been really hard work. With the recent rains everything looked lush, with waterfalls coming off of the sandstone caps on top of the ridges bracketing the creek. The wildflowers were all out, including some that we'd never noticed before. The creek itself was almost a seagreen color from carrying what I'd guess is fine sediment, almost like rock flour in some northern rivers. Fishwatching wasn't an option. We also played with the butterflies which were thick along the creek as usual this time of year, landing on damp soil to lick salts, etc. I'd almost forgotten just how beautiful the Wilderness is.