Tuesday, April 28, 2009

We Finally Got Back To Limestone Creek Yesterday

We did a quick jaunt out to Limestone Creek along Mooresville Road yesterday after I gave my second freshman biology final exam. The day was totally clear, about 80 deg. F., and the water was fast-flowing but not threatening. Taito, Brittany and James went along. We were able to capture 20 adult scarlet shiners, including one super-alpha male. I also used an aquarium net to capture about 20 very small, days-old scarlets, ranging from ~7 - 12 mm long. The pigment pattern is very distinct even at this age, so I'm sure they're scarlets. James set up the driftnet and we let it collect drift for about an hour. I hope to make some digital microscope photos of the young scarlets soon.

Sunday, April 26, 2009

Hillabee Creek On Friday

I spent Friday driving down to Hillabee Creek in Tallapoosa County with Stan Sung, Tom and his sons from Connecticut, and Andy and John from California. We hit the beautiful spot near Alexander City. We netted some stippled studfish, of course, and a range of other fishes and turtles. The riffles there are full of muscadine and speckled darters, but we didn't see any lipstick darters. The Tallapoosa shiners were just beginning to go in to color, and the pretty shiners were about as colorful as they get with irridescent green on the males. Photos will appear later, I let Stan and Andy do all of the photos on this trip. The funny part of the trip was watching local dudes drive their trucks out in to the creek, and then work their way up a rutted dirt road going up a low hill by the stream at about a 60 degree angle, drive around a short loop road on top, and drive back down. Times are slow, I guess. At least we didn't find any recently executed dogs under the bridge there.

Wednesday, April 22, 2009

Estill Fork Is High, Fast Water

But even with high water we were able to catch a reasonable number of telescope and scarlet shiners today. We even netted a lamprey (brook?) and a sawfin shiner. While we were seining an installed drift net captured a surprising amount of material, including large number of springtails and pycnogonid spiders.

The creek was over the bridge in a small rivulet. You can see it in the middle of this picture:

James did the honors with the water chemistry testing today. The pH was 7.0 compared to a typical value of about 7.8, the result of dilution by lots of rain.

Here's Andrew ready for action with the seine, attired in a snappy World of Warcraft sweatshirt.

Andrew set up and emptied the drift net, shown in the photo below. The heavy tomato stakes I got for staking the net into the stream bed aren't up for heavy flow days like today. But Andrew got the net installed in an area of lesser flow, even with a floppy tomato stake. The water he's standing in looks mild, but the flow rate was probably 12-15 knots. In the riffles it was much rougher, and deeper.

And finally, here's a view of the primary riffle site. It doesn't look like much with the high water, but the scours were even more pronounced than normal. Water was probably almost a meter higher on Monday, I would guess, based on the wrack lines up the banks. In truth this is probably closer to what the stream should look like given normal rains, which we haven't had for several years.

And if you were wondering, the darters were all colored up today. We found a species I've never encountered at this site before, the stripetail darter, Etheostoma flabellare. The fish was an adult male in breeding condition, including the egg mimics on top of each spine in the first dorsal. Neither James nor Andrew had seen one before, so they were suitably impressed. The egg mimics seem to entice females to spawn, since females are stimulated by the presence of eggs in a male's nest under a mussel shell, for instance. For that matter, I'm suitably impressed too!

Tuesday, April 21, 2009

It's Stopped Raining, Back To The Creeks!

I had to cancel another trip to Limestone Creek yesterday when I realized that we'd received well over an inch of rain on Sunday. Hopefully we can get there, once and for all, next Monday. Tomorrow we'll go out to Estill Fork which is far enough up the system that it should be mostly drained from Sunday's severe weather. And on Friday I hope to go with Stan Sung and Tom Ganley to Hillabee Creek in Tallapoosa County for a viewing of stippled studfish, etc. Meanwhile, final exams begin on Thursday and will be done for me next Tuesday. That last exam is the Vertebrate Zoology final which will take more work to read and grade.

Much of yesterday I spent working on the black darter article. This involved formatting it for submission to the Journal of Fish Biology which has very exacting format requirements (I rarely use the word "colour"). The one last hurdle now is to re-format all of the photos and figures into high-resolution formats, TIFF with LWZ compression for the photos and EPS for the figures. Since I have Photoshop it's not all that hard, I just have to guess(?) correctly for the right image size. The publisher has some very nice explanatory documentation but it's still ambiguous at key points. The worst the editor could do would be to say "no", and then I resubmit it...

Saturday, April 18, 2009

I Received & Mailed Out The New Primers

I'm grateful to IDT in San Diego, the primers I ordered on-line Wednesday arrived yesterday and I mailed them to Phil Harris in Tuscaloosa first thing this morning. If this makes the sequencing work I'll be both relieved & happy.

I had to postpone our trip to Estill Fork yesterday. The painters were just finishing work on our house, and I agreed to hang around and make the payment to the contractor. They did a good job, but my wife just didn't want to deal with a bunch of guys one last time. The crew leader turns out to be a rabbit breeder and couldn't understand why we wouldn't give him some rescued young house rabbits we just took in. As with most breeders the concept that there are too many rabbits being produced for the local market is totally bizarre. But, that's the root of pet overpopulation problems. Blah. Anyway, we hope to get out Monday morning since there are no classes; finals begin on Thursday!

Wednesday, April 15, 2009

Good News, Bad News On Bifax Sequencing

I talked to Phil Harris from UA Tuscaloosa today. They tried to sequence our stippled studfish DNA, but it didn't work. Their determination was that the extractions themselves are OK, but the sequencing primers we gave them aren't any good. The latter is the relatively minor bad news. I bought them last November from our local supplier, whose reputation has been going bad for a while. I ordered a new set of primers today from a place in San Diego recommended by Phil, IDT. For a total of $33 I'll get the primers next week, and ship them in lyophilized (dry) form to Tuscaloosa for them to resuspend. So there's hope. I was afraid our purified amplifications wouldn't be good, which is a deeper problem. So if it all works just with getting quality primers I'm happy, and also grateful to Phil's group.

We still hope to get out to Estill Fork Friday afternoon, it hasn't rained since Monday!

Sunday, April 12, 2009

More Rain's Coming, So No Limestone Creek Trip This Week

The north 'bama forecast is for an inch of rain tonight, and another inch tomorrow. So I doubt we'll do a trip on Wednesday since this site on Limestone Creek is low in the drainage. From past experience it will take at least 4 or 5 days to drain. But, hopefully we'll get out to Estill Fork on Friday, which is way up its drainage so I don't think that will be dangerously high water.

Saturday, April 11, 2009

Skunked By High, Fast Water

Yesterday I was able to convince James & Alexandra to join me for a quick scarlet shiner collecting trip to lower Limestone Creek about 12:30. The challenge was a severe tornadic system approaching... but I hoped we could get there, collect a dozen or so scarlets, and flee for cover back to UAH. When we got there I immediately realized we were out of luck. The creek was a good foot or more higher than when we were last there in January or early February when I thought the water was high, and the water was whipping through. With those conditions we weren't going to make a quick collection, and I didn't want to hang around in dangerous water with approaching severe thunderstorms. So we cut and ran. Watching the storm on weather radar from the safety of my office, one of the most intense centers of that storm went right over that creek site about 90 minutes later and then hit us at UAH. We didn't get hail, but a friend near campus had golfball sized hail hit her house. Oh well, maybe next Wednesday? The weather gets better next week.

Alexandra and Taito, working with Ernie in the Bishop lab, ran a test Western blot of homogenized shiner brains this week. It came out surprisingly well, with mostly well-defined bands. We didn't have a good protein size standard running with it, but it augurs well for future Westerns to compare NMDAR levels in various fish. The one tech fix we'll do is to use monoclonal rather than polyclonal antibodies for even sharper resolution of molecular weights of brain proteins. Alexandra is all excited to do more of that over the summer; sounds good to me. The whole point of this will be to compare brain functions between sexually dimorphic scarlet shiners, and much less dimorphic telescope shiners. It should be fun!

Thursday, April 09, 2009

Running Western Blots, Better Mummichog Cladograms

We're finally running the first test Western blot on brain tissues from scarlet and telescope shiners from the early winter. We're trying to measure the amount of an important subunit of the cellular membrane protein NMDA, a key channel for learning (and sex) for vertebrates like fishes and ourselves. This first run probably won't work too well since the lab group doing it haven't used this exact protocol. But on Saturday they hope to spend the whole day running a better calibrated Western so we can get reliable data. The fish in this experiment include young-of-the-year individuals, and I'm not sure what to expect with their NMDA levels. With any luck this will be the beginning of a lot of work with Westerns. We're going out to Limestone Creek tomorrow for a seasonal collection of scarlet shiners, in part for some NMDA tests. I hope to be able to wade without waders since the temperature is now in the 70's F for several days.

I met with Kris yesterday, and his cladograms of mummichog DNA are even better than before. For creating a neighbor-joining tree he ran 10,000 bootstrap replications, which indicates the confidence you can place in a tree. Several of our nodes are supported at the 100% level (all 10,000 replications showed these nodes), and the weakest one (separating the Charleston & Sapelo Island, GA, fish from the Virginia Beach & Chincoteague, VA, fish) is 63%. It's not really surprising, but I feel even better about what we've found and its interpretation (a strong founder effect for the post-glacial recolonization of the northeast as the ice retreated starting about 14,000 years ago and climate moderated).

Monday, April 06, 2009

A Few Quick Thoughts

I noticed some things at the ASB meeting in Birmingham that I'm still cogitating about. The first, relatively trivial, is no meeting t-shirt; I'll admit that I'm a sucker for meeting shirts. Maybe linked to this is the observation that people were unusually well-dressed at the meeting, with a surprising number of guys wearing ties (not me...). And I didn't notice any obvious reporters at the E.O. Wilson speech, although I could well be wrong about that. I still have the old Yippie idea that all press is good press, and as biologists we certainly have to keep beating the drum about the growing biodiversity crisis.

Tomorrow is Convocation Day at UAH, with various honors bestowed on various faculty and students. Brittany will receive recognition as the top undergraduate student in the College of Science. She certainly deserves it, and I'm happy for any and all reflected glory.

Friday, April 03, 2009

Fun At ASB

We just got home from the ASB meeting in Birmingham, a 27 hour trip with thrills and chills. The chills part was leaving yesterday as a heavy band of thunderstorms approached Alabama from Mississippi and closed in on I-65, our route to B'ham. South of Huntsville, on a secondary highway, we went through a near white-out of heavy rain and pulled over for a few minutes. Then we raced on as the rain subsided, and got on to 65. We heard on the radio that a tornadic storm was forming and running through the area we had just driven through. And, we listened to descriptions of storms running through the Huntsville area; luckily the worst ones missed our house, and also missed the UAH campus.

Once we survived and got to ASB, things went well. My talk this morning on telescope shiner reproductive biology was the first one I've done at a conference that I finished gracefully within 15 minutes, and had time for a question. I said just about everything I meant to say, and avoided any random faux pas. Two other talks in the Herpetology/Ichthyology session were interesting; Michael Sandel from Tuscaloosa presented part of his dissertation work on pygmy sunfish species distribution and population structure as a likely result of the waxing and waning of glacial cycles that affected sea level along the Gulf and southern Atlantic coasts. And Josh Turner from Jacksonville State University in AL gave a presentation on the current status of the holiday darter in AL; in short, the species is found in several stretches of Shoal Creek in the Talladega National Forest in Cleburne County, and those stretches are cut off from each other by small reservoirs that fishes can't traverse, certainly not upstream. The Forest Service is aware of the situation, but is probably unable to break down more than one of the three reservoirs in this chain. The species is also found in Georgia, but isn't exactly common. It's a variation of what we've found with the stippled studfish in the Tallapoosa River system, not a big surprise unfortunately.

This afternoon there was a Symposium on Darwin, observing his 200th birth year. Several good speakers were part of it, including Andrew Berry from Harvard who has a wonderfully sick British sense of humor and talked about the possible replicability of evolution if "the tape of history was rewound", as Stephen Jay Gould put it. But the capstone was E.O. Wilson ("Ed" to his pals), speaking on his 80th birthday today. I hadn't seen him for years, and he was good (and frailer looking). He spoke largely on how bad the biodiversity crisis is becoming, as most people care about saving the physical environment but not the biosphere. He urged students to study nematode worms or fungus, because both groups, as examples, are hugely understudied and anything you find out about them is new; both groups probably include millions of as-yet undescribed species. His best description was of the human condition: we have stone-age emotions, with medieval institutions, and God-like technology, all in all a dangerous condition.

It was good to get out and see some people I haven't seen for a while, and hear about various research projects. And that's what's good about going to scientific mettings!

Thursday, April 02, 2009

Goin' To ASB Today

I'll teach my classes today, and leave for the ASB meeting in Birmingham this afternoon. My talk (all 15 minutes of it) on the reproductive biology of telescope shiners is scheduled for 9:15 tomorrow morning. One important question is what to wear during the talk; I'll go with a the NANFA shirt from the North Carolina convention with a nesting male bluehead chub on the front, I guess that's my version of colors at this point (maybe it should have a 1% patch on the front?). I'll miss being a judge at the state science fair tomorrow, which is hosted by UAH. Kris will lead a small team of judges in the animal biology section in my place.

The Enrique thesis is currently distilled down to 22 pages including an unedited Discussion. I hope to give the current version to Amy to read for anything I screwed up in the Methods section, especially, since I'm not an ace with Western blots or their interpretation. The Results section was surprisingly good, just two pockets where I eliminated blocks of two or three paragraphs that basically repeated text from the Methods section. We have five figures, which I think is the absolute highest number we can go with. That might be our toughest editorial decision.