Saturday, February 27, 2010

Reorganized For Brain Measurements, DNA Sequencing

I met with Joe, Andrew, Taito and Brittany yesterday afternoon to take stock of where we are after the last two weeks. Ernie has offered to help us do Western blots for NMDAR assessment of non-reproductive season fish, so Taito and Andrew will work with him. We may be able to use a simplified blotting process that Ernie has brainstormed which would be good, but still needs testing. We've lost February as a month in Brittany's study of driftnet contents, but we'll just pick up in March with the next new moon on March 15. Brittany has also offered to work on measuring fish brain size while waiting for more driftnet material to ID. We'll go out this Friday to Limestone Creek to collect scarlet shiners for NMDAR analysis, the last piece of the puzzle. And hopefully as of Wednesday we'll have cleaned up PCR product for 9 individuals to take to Operon for sequencing as a first test of Joe's work on the stippled studfish project. As usual I'm hoping for the best, and I think it will actually work.

This is my 400th post here. And I don't even have a snazzy new photo to post!

Sunday, February 21, 2010

A Hike Along Borden Creek Today

Ruth and I took advantage of a beautiful early spring day to escape to Borden Creek in the Sipsey Wildnerness of the Bankhead National Forest. This is a devastatingly beautiful area, and we both needed to hike down the canyon trail along the creek. The specific trail we took is on the west side of the creek, which is more challenging than the east side trail. But it also leads to and over some fun sandstone formations.

The first shot is me standing on the beach near the trailhead where we've often set up a basecamp for fishing operations. Creek level was a lot lower today than when we were there three weeks ago to seine silverstripe shiners. And the water was pretty clear, too.

The next view is from the large cube of sandstone we climbed up to have a picnic. It's about 1.5 km down the trail from the trailhead. This rock is connected to the bank by a low hump of gravel and cobble that was dry today. The creek is forced to run around this rock through a narrow neck of water that's a fast-flowing run loaded with schools of shiners. We've hung out on this rock before, once observing a huge school of redhorse suckers engaged in some sort of spawning ritual. Today it was a perfect place to sit in the sun and wonder what the hell just happened.

This is a stretch of creek about halfway between the trail head and the sandstone cube. I was struck that it would be a good place to run another driftnet project, since it's reasonably shallow and runs over both rocks and sand to maximize the presence of macroinverts. Hopefully the Forest Service biologists would agree to sanction such a project.

And the last view is what the bank across the creek from the sandstone cube looks like. I was struck that the wave riffles on the sandy bottom continue up the steep sandy bank which was recently under water. At the top of this photo you can see evidence of recent high water way up the bank in the form of streaks of leaves deposited by high water. These headwater creeks are dynamic places.

So I feel a lot better after spending the day along Borden Creek. Walking on the sandy trail, jumping across deep-cut narrow water gutters running out of sandstone crevices across the trail, seeing big schools of silverstripe shiners, and seeing a kingfisher go whipping by us just above the waterline were all some of what both Ruth and I needed. And I didn't even include any of Ruth's butterfly photos!

Wednesday, February 17, 2010

Thinking About Fish, Etc., Again

Five days post-shooting I really feel like I want to re-start my life, like for instance finishing the revisions of my flame chub manuscript. I've felt like an apple on the flood for several days, not sure where I should be, when, for what. The Shelby Center is no longer a crime scene so I can go to my lab to feed the fish without a police escort. The 55-gal. tank with orangespot sunfish is in dire need of cleaning but I haven't been there long enough to do anything. Tomorrow the funerals begin, basically one a day through Saturday. At least Roger, who took a chair-back-slowed-down bullet in the chest, is back up and around with essentially a bad bruise around the rib that took the bullet impact.

I look forward to seeing Estill Fork or any other stream sometime soon. And I'm grateful to all the people, from Australia to France, who have written with concern and support for our well-being. To use the Latin, pax vobiscum.

Saturday, February 13, 2010

I'm Still Here

I survived the shooting at UAH yesterday. It was as horrible as you might imagine. Largely by the luck of being on the far side of the room from where the shooter was I avoided injury. Others weren't so lucky and that's the horror. I look forward to posting about fish sometime in the near future.

Sunday, February 07, 2010

The Plan For The Dimorphism Manuscript

The best idea seems to be to forge ahead with examining the brains of non-reproductive individuals, and combine that data into our current manuscript so that we'll have both reproductive and non-reproductive data for a stronger story. Whatever we find is interesting: either there are pronounced seasonal changes in brain structures, or there aren't. Both outcomes imply fundamental organizational processes for cyprinid brains, and I still haven't found other research looking similar phenomena. So, it's on to more western blots for NMDAR, and more brain dissections for overall size.

Today I sat down and wrote up my thoughts on all of this year's NANFA Conservation Research Grant proposals. The eight of them are the strongest group we've had yet, and I could only exclude two of them for not being as strong on conservation impact as the others. I sent my thoughts to the other two members of the committee and I'm waiting to see if their basic analyses match up to mine.

Friday, February 05, 2010

Wow, A Quick Manuscript Decline

I'm impressed by the editor at Behavioural Brain Research. It only took him about 28 hours to politely pass on our dimorphism manuscript. It was an interesting turn of phrase, below:

"This is to acknowledge receipt of your manuscript. I am sorry to inform you that a preliminary review of your manuscript by members of the Editorial Board found that the subject of the paper is not a high priority for Behavioural Brain Research. Due to an increasingly high number of submissions, and a large backlog of papers awaiting publication, we are at present accepting only manuscripts with an initially high priority rating. I am sorry about this negative evaluation and hope it does not dissuade you from submitting contributions to Behavioural Brain Research in the future."

We don't suck, they're just not interested in the topic. I now realize that this is likely to be true of all neuroscience journals; they're interested in a very narrow range of hot topics, like stem cells or apparently anything to do with mice. Our work is too interdisciplinary, about several obscure species of freshwater fishes. So, for our next move, I think we're going to submit it to Freshwater Biology. They're more of an applied ecology journal who have always had broad interests. I guess we'll test this perceived broadness. Have they ever published an article that uses western blots? I honestly don't know, it should be interesting...

Thursday, February 04, 2010

Our Sexual Dimorphism Manuscript Is Submitted to Behavioural Brain Research

This submission took about an hour this morning, registering for a password and going through a series of steps to submit the right things in the right order. But it's in... and I only made one serious screw-up that Andrew just pointed out to me. We have three Figures that have to be submitted separately because they have to be high resolution TIFFs. I submitted our Figure 2 twice, with no Figure 3. So I just wrote to the publisher's office and asked how I might submit the real Figure 3 with the manuscript for consideration. I'm sure that's happened before, but I still feel foolish. Gack!

Our lab group is meeting tomorrow afternoon for the first time this semester at 3. We have enough deep-frozen fish now that we can move on to extracting brains and setting up western blots. Hooray, real science!