Sunday, January 31, 2010

We Found Silverstripes At Borden Creek

Today was a clear, not horribly cold day after rain and ice off and on over the last several days. On the last day of my permit from the Forest Service we went to Borden Creek in the Bankhead National Forest to collect silverstripe shiners for our study of fish brain size and structure out of breeding season. Here's a view of typical silverstripes we found; many were bigger than these.
Today was definitely a waders day. It's an awkward thing to put them on in public as Taito and Andrew are doing here. The banks along the creek are mostly sand, the remnants of ground-down sandstone and limestone.
The creek was high and fast, but cutlines along the sandy banks showed that the level had been up at least a foot in the very recent past. The water is carrying enough sand that it has a greenish color, below. We caught fish below the riffle at the right of the photo.
A group of backpackers walked by us as we were doing our last seines. One guy asked the classic question: "Are you fishing?" It was all I could do not to say that we were racing submarines... Later, on our way out across the bridge, the backpackers were sprawled out in the sun. They asked why we were collecting the fish, and I told them that we were examining the brains for evidence of changes related to sex and reproduction. I think four out of five of them let their jaws drop. I was able to point one of them upstream to a series of deep holes since he wanted to fish for coosa (redeye) bass. I've seen them in years past in these holes at the base of large boulders, and I'd guess that they're there today. We left before we saw them catch any, I hope they did.

Wednesday, January 27, 2010

Lookin' Good On The DNA Front

Joe came by this afternoon to test the quality and concentration of the bifax PCR work he did last week using just a single primer in the reactions. It came out at much higher concentrations, with better ratios and spectrophotometric properties, than what we'd been doing before for which I'm happy. Next week he'll move on and PCR these amplified samples using the other primer, and if they look good we'll have those six samples sequenced to see how well they turn out. And if that works then we'll attack the remaining 32 or so samples. I keep thinking this should be easy but at least for me it hasn't been, in a future life maybe I'll be a for-real gene jockey.

We hope to go out this Sunday to Sipsey Fork on the last day of my collecting permit and snag another group of silverstripe shiners for brain examination. Four of us are going, which will be good for dealing with cold, fairly high water. But this time the temperature shouldn't be worse than the low 40's, almost balmy compared to our last trip.

Kris came by to talk about his thesis with the mummichog DNA. It's just about done for once and all, and next week he should be able to give full review copies to all members of the committee. We're aiming for his defense on Feb. 24. It's a concise, short thesis as part of our new campaign to cut out extraneous verbiage from theses. Basically, we reinforce previous work on mummichogs showing a north/south population split, and identify 16 SNPs in the cytochrome b gene that are informative for defining haplotypes. In the south population there's a subdivide between Virginia populations and South Carolina/Georgia populations, with the Virginia populations showing SNPs that change the first codons of three amino acids, two of them for a different amino acid. Given that this protein is a key part of the mitochondrial electron transport chain this is interesting stuff. We don't know exactly what function(s) may change, that's beyond the scope of this work, but it would be good to follow up with crystallographic studies. I hope that we can get this work published, maybe in Northeastern Naturalist.

Friday, January 22, 2010

Estill Fork On Jan. 18

Taito took a bunch of good pictures of our trip to Estill Fork in Jackson County last Monday. Here are two of the shots.

The low bridge across Estill Fork was overwashed from about 5 cm of rain the previous two days. The site was historically a ford, so it's almost going back to nature during events like this.
Pulling the net in high water was physically challenging, so we took a few breaks. Here's Brittany, me and Andrew lounging on what's usually a bigger island.
We'll return on the new moon next month.

Wednesday, January 20, 2010

The Flame Chub Manuscript Has Been Accepted

I heard today that my flame chub manuscript has been accepted by the journal Endangered Species Research. The three(!) reviewers all had positive things to say along with constructive suggestions, one of them even explicitly liked the interactive flame chub map that's part of the story. So hopefully I can get this turned around in a reasonable amount of time and get it posted on to their web site which (I think) is how they proceed.

On the other hand, the journal NeuroReport gave us the final blow-off for the shiners NMDAR article. The editor included one statement that confirmed my worst fears: he was afraid his readers wouldn't be interested in the work. My fear was that our work involved too much ecology ("real biology") in a very reductionist field; we aren't just studying one molecule in isolation but relate it to reproductive success and strategy. So, with some relatively minor reformatting we're going to resubmit the manuscript to the journal Behavioural Brain Research which more explicitly expresses interest in work that relates organismal behavior to some aspect of neuroscience. "Interdisciplinary" research is all the rage in academia, but god help you if you actually try it. I had a t-shirt years ago that summed up my attitude on the subject: Fark them if they can't take a joke. I would send one to the editor at NR, but I don't think he'd either get it or appreciate it.

I hope to post pictures soon from our Estill Fork trip on Monday. The water was a good foot deeper than before, with much faster flow, but we still managed to seine 6 telescope shiners for (what else?) western blots to assay NMDAR levels. And, we caught and kept a small lamprey that I have in an aquarium to show to the Vertebrate Zoology class. Running the seine in that kind of flow was my best upper-body workout for the month!

Friday, January 15, 2010

Back To Bifax DNA, Maybe On To Providence, RI?

A new student at UAH, Joe, is going to work in the lab to reamplify and generally groom the bifax mtDNA we've tried to sequence. I received a new polymerase kit from New England BioLabs yesterday, so we're about ready to go. The trick is to further amplify, and then perform a linear amplification, kinda like we didn't do before. So hopefully this project is back on track in the midst of the neuroecology, parasites and driftnetting.

I've been thinking about going to the ASIH (Ichthyology) meeting this July in Providence, RI. I like to go to ASIH every coupla years, anyway, and I'm due. My immediate thought is to do a talk on our NMDAR findings, and a revved-up poster on Jennifer's 11-KT scarlet shiner work. I haven't been back to New England for years now, so Providence could be fun. It's an interesting old, well-lived-in place.

Sunday, January 10, 2010

Black Darters R Us

I keep making passes at editing down the black darter manuscript so I can send it back to my editor for Southeastern Naturalist. It's almost ready, now that I've gotten rid of almost half of the Methods and collapsing much of the Results into a Table reporting significant ANOVA results for various comparisons between sexes, months, and the two sites. Including all four Tables that are now inserted in the right place, and two Figures, it comes to 27 pages total compared to the original 39. Scientific writing is all about taut writing, and this manuscript has staggered in that direction. I want to read it front to back one more time before kicking it back.

One goal for the semester that begins tomorrow is to crank out and submit a manuscript on the Dactylogyrus parasites of telescope shiners in the upper Paint Rock system. Andrew has to make one last push to count parasites in our November and December collections, completing our twelve month observations. The November group is mostly finished, and I mentally calculated an average 1.4 parasites per fish from looking at data in the lab book. Andrew and I have agreed that this will be a de facto scientific writing class with him as the lead author for writing the manuscript. And Taito will do an Honors Research project this semester, I think focusing on the brain measurements and western blots of NMDAR for non-breeding silverstripe, telescope and scarlet shiners being collected this month.

We go back out to Estill Fork next Saturday. Luckily the current deep freeze is supposed to let up tomorrow and the rest of the week.

Wednesday, January 06, 2010

Yeah, It Was Freezing At Sipsey Fork In The Bankhead National Forest

And, I have the pictures to prove it. Taito and Andrew joined me going to the canoe launch to collect silverstripe shiners WAY out of breeding season. The water level was higher than last July but manageable, and the current was faster. It's been so cold locally that the fine white sand on the bank was frozen solid, making for more of a challenge descending to stream level. In about an hour of seining, we managed to catch about a dozen silverstripes, mostly small ones, and two or three burrhead shiners. We had to break up fringing ice along the banks to pull the seine up, and if the seine was left out of the water for any period of time it would freeze solid. Air temperature was about -5* C, and water temperature was 2* C. Unfortunately, my old waders that Taito was using leak so he had to get out of the water. After about 30 minutes sensation returned to my hands, and we had found the best stretch of bank to seine for fish. Then, as we were walking the seine back to shore with what turned out to be a large burrhead, my left foot lost traction in the loose sand in the water and I fell to my left, soaking my left arm and shipping some water in my waders. That was the end of the day... I took off my shirt and sweater, and put on my coat over my wet t-shirt. This was as brutal as it gets locally. The fish are all in the deep freezer now. We'll go back to them later to remove their brains. We still have to collect telescope and scarlet shiners from Estill Fork next week, when the weather should return to a more normal, moderate range.

Anyway, here are some pics of the scene. The first one is icicles hanging from the sandstone cliff across the stream from our access point. You can see how clear the water is now (it usually is, even in summer).
I have a series of pictures of the view downstream from this point; this one is different with ice along the shore. The sand along the left is solid...
And finally, a shot of me looking colder than I realized after having stripped out of my soaked shirt and sweater. It was one of the rare times I wear a hat around here.