The Plan For The Dimorphism Manuscript

I talked to Amy yesterday about what we should do with our recently declined sexual 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.

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. Amy and 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...

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!

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.

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.

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.

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!