Sunday, August 27, 2006

Lining Up Students For Research Projects

Now that school has started, I'm running around like a crazy person to teach my two Biology 1 lectures and Vertebrate Reproduction. The Vert Repro class will largely use fish as examples of vertebrate reproduction, so that should be fun. I now have 34 students in the class, by far a record. They seem to be sharp; tomorrow we discuss our first journal article-based example, a classic paper by vom Saal et al. from Science in 1983 on the effects of embryonic exposure to estradiol in mouse pups. Basically, those male pups with higher exposure seem to be more sexually active and less aggressive; "I'm a lover, not a fighter"?

As well as terrorizing undergraduates with serious endocrinology, I have students starting and picking up various projects. Leigh has agreed to do a project to characterize certain neurons in the scarlet shiner brain. I realize that I've started to make the scarlet shiner a model study animal but the species could be good for that. If Leigh is good at dissecting out intact shiner brains, this could be good. The carotenoid pigment extraction project I was thinking of we'll probably do next spring on a representative sample of scarlet shiners. It should tie in with both Leigh's project and also Jennifer's project to characterize testosterone levels in scarlet shiners, and relate that to digital analysis of body color. It's all a lot of work but I'm excited because it's a true integrative biology project, looking at an organism on a bunch of different levels to understand how it makes its living.

I've also accepted an invitation to do a talk on my flame chubs project to an Honors science class offered by the Physics department on campus. The teacher wants a range of scientists at UAH to talk to the class about their research, as an example of how the scientific enterprise works. It's a good excuse for me to pull together all of my data, thoughts and pictures to explain why this project is interesting, and what I've found. I think it's Sept. 25 that I agreed to do this.

Wednesday, August 23, 2006

RIP John Bondhus

John Bondhus died this past Sunday, Aug. 20, from an infection he wasn't quite able to shake. John was the central organizer of the North American Native Fishes Association (NANFA) in 1972. He and a small group of other native fish enthusiasts worked to establish a group to advocate for native fishes and their enivoronments, and to support the responsible aquarium keeping of many of these fishes. NANFA has withstood many storms and stresses over the past 34 years. Today we have 480 members, and produce a high quality quarterly journal, American Currents. All of us in NANFA will miss John, who was always a quiet, rational voice especially at key moments.

In other, happier, news, an undergraduate has agreed to work with me and Amy, our departmental neurobiologist, on an interdisciplinary project to characterize certain features of brain cells and regions in scarlet shiners. This project will stain and section brain tissue with antibody stains to examine differences between male and female individuals in a key neurological pathway related to both learning and sexual differentiation. I've never worked on any kind of immunohistological project so much of this will be new to me. The project relates to what Jennifer is already working on, characterizing pigment intensity and testosterone levels in scarlet shiners. I never thought of making scarlet shiners a study animal, but they lend themselves to it in several ways. They're a common species, so we aren't destroying local communities, and they also have pronounced sexual dimorphism enabling the study of what shapes and guides the dimorphism. The beauty of it all is that we're linking cellular and molecular processes with sensory ecology. It should be fun!

Friday, August 18, 2006

Hey, Wanna Do Some Freshwater Fish Research?

This is my first offer, which I'll follow up with more in-depth propaganda. If you or anyone you know wants to do a Master's of Science in Biology with a research project involving North American native freshwater fishes, please contact me. This would be in the Department of Biological Sciences at the University of Alabama in Huntsville, in the Tennessee Valley. One would need an undergraduate degree, of course, preferably in the sciences but that can be finessed. I could offer support of a stipend with tuition remission for working as a Teaching Assistant, probably in our freshman biology courses. I have a number of ideas for research projects, any of which could be done in a two year period I hope. Our department is moving to a brand new science building in a year, so our facilities should be posh on the scale of things and, even better, I'll have a new improved lab. Feel free to call me at 256-824-6992.

In this quiet week before school starts next Wednesday I've rewritten my manuscript on burrhead and silverstripe shiner reproduction. It's shorter, tighter and all around better, I hope. Before I submit it to Southeastern Naturalist a colleague who's a plant ecologist has offered to read it to catch any glaring glitches and misstatements. Then, off it goes. It's almost enough to make me pray!

Monday, August 14, 2006

Scarlet Shiners, Courtesy Of Phil Kukulski

Phil Kukulski from Michigan updated me on the scarlet shiners he collected near Athens, AL, last winter. That trip was a major adventure for cold, falling in water, etc., but he survived. The scarlets that he has raised have spawned in the last several weeks. Below is a photo from that tank, with a male in breeding coloration in the foreground:

Below is a photo of some the newly hatched fry he found in his tank. I realize that I've never seen scarlet shiner fry before. They look like other newly hatched cyprinids, of course. But it's still interesting just because now I can say I've seen these fry. Phil's breeding tank set-up was very simple, a 10 gallon tank with a powerhead trained on a pile of small stones in the middle.

I've heard rumor of some researchers from Ohio, I think, starting a research project on scarlet shiner life history. But it would be an interesting project in north 'bama, since most local creeks are loaded with them. And thanks Phil for sending the photos... they are copyright Phil Kukulski, of course.

Friday, August 11, 2006

Carotenoid Extractions Might Even Work

I spent part of the day today re-reading how to extract and measure carotenoids, for the purpose of directly measuring the physical display of male scarlet shiners (as suggested by Brady Porter). Carotenoids have historically been of interest to plant and fungal biologists more than animal biologists. The comprehensive discussion of the chemistry and handling of carotenoids is in a compilation for plant biochemists entitled Chemistry and Biochemistry of Plant Pigments, Vol. 2. Carotenoids can be extracted by soaking the tissue of interest in absolute ethanol; then, the trick is to concentrate the hydrophobic pigments in petroleum ether which is nasty stuff to handle. But I think it could work and yield interesting information. One student I know wants to do a Special Topics/Research class this fall; now I have to figure out if she's up to this kind of biochemistry.

I also finished assembling the readings for my Vertebrate Reproduction class. Instead of a textbook I have 29 readings in .pdf format, and several photocopied chapters from various books. It won't surprise most of you to know that I'm using fish as a model organism for vertebrate reproduction, since they have the same basic processes and functions as the tetrapods. I'll especially be talking about various aspects of sexual selection using guppies as a primary study organism, since there's a surprisingly large literature on the subject. My end unit is on naked mole-rats, the only known eusocial mammal. Their social structure is more like honeybees than typical mammals. They're so weird by our standards that talking about them serves a useful purpose.

Tuesday, August 08, 2006

Things Are Slow At The Moment, But Not For Long

Now that summer school is over, various students working on projects with me have scattered until school starts again on Aug. 23. But I think we'll get out this Friday to collect more striped and scarlet shiners in Limestone and Swan Creeks. Jennifer's foot is still fugazi but I think we can do something anyway.

I've also swung a deal with a graduate student whose focus is bioinformatics. He needs support this fall, so he's agreed to teach three lab sections for our Biology 1 class. He has experience teaching Organic Chemistry labs, so this should be easy (I hope!). As he wraps up his work here he only needs one more formal class. But in order to teach as a fully supported Teaching Assistant he has to be registered full time. So, I'm setting up a Special Topics class for him to take and the project will be making sense out of my set of DNA data from Fundulus heteroclitus, F. similis and F. majalis. I've had these mitcohondrial cytochrome-b sequences since last December but haven't been able to get at them. The heteroclitus data are from populations along the Atlantic coast from Boston Harbor in the north, to Nantucket, and down to Charleston, South Carolina. My question is whether the Nantucket population shows any genetic differentiation from other populations after almost 8,000 years of being isolated by rising sea level. I've been working on this since 1996, so I'm not in a blistering hurry. The other sequences, of similis and majalis, are for assaying the genetic similarities of these two very similar species of coastal killifish. I have access to sequence data from majalis I collected in Boston Harbor, Nantucket and Charleston, SC, and I've collected similis along the Florida and Alabama Gulf coasts. Early results with few localities (Boston, MA vs. Dauphin Island, AL) showed interesting differences. I hope it takes less than another ten years to get more information.

Here's a strangely informative photo of F. similis. The fish are pretty much black and white in life. You can see, I hope, why they're variously called the longnose killifish or the tiger minnow.

Below is a mummichog, F. heteroclitus, with silly caption. I've always been fascinated by this species which is overwhelmingly common in Atlantic coast saltmarshes from Newfoundland as far south as north Florida.

Thursday, August 03, 2006

Map Development And My Current Flame Chub Tally

I'm wrapping up the summer school semester this week, giving my Biology 1 final exam tomorrow morning (it's easy, really!). I've also paused to tote up and appraise where I am on the flame chub distribution project. Yesterday I had the time to sit down and read through my field notes to count up sites visited, and flame chub populations found. I have a correction: I've actually visited 50 historic collection sites rather than 47, and found flame chubs at 18 of them, for an apparent 64% stream range reduction across north Alabama. The 50 sites visited represent 85 of the 151 museum collections at the University of Alabama Ichthyology Collection. So, I think I've hit a reasonable sample of the sites available. I've also visited several sites where we weren't able to do a real sampling, such as Big Spring Creek in Blount County (difficult stream access and large woody debris in stream), Wheeler Spring in Lawrence County (beaverdam raising water level too high) and Pickens Spring in Limestone County (unable to gain landowner's permission). Plus, I've found four previously unreported flame chub site locations: French Mill Creek in Limestone County, Limestone Creek in Madison County, Paint Rock Creek in Marshall County and Hurricane Creek in Jackson County.

I met with Kevin yesterday in his office to discuss developing various GIS-based maps in ArcView to represent my results. The end result will be clearly annotated large wall maps, at least 3 ft. X 3 ft., and smaller, simpler maps for publication purposes. When I get one of the latter I'll post it here as a fer-instance.

A good case can be made that flame chubs have undergone a significant range reduction over the last 40 years or so in north 'bama. My results don't include the apparent extirpation of isolated populations of flame chubs to the SE of north 'bama from several springs in Talladega and Calhoun counties, fairly close to the city of Anniston. The huge question remains just what's causing these local extinctions. Local human land use decisions certainly are a big part of it, but maybe not the whole story. Are flame chubs somehow more sensitive to some other changing parameters, such as local climate changes including rainfall patterns? It sounds plausible but I certainly don't have any evidence for it. I'll leave you with that thought.

Tuesday, August 01, 2006

I've Overcome More Species ID Doubts

The last two days I've been going back and forth about whether some flame chubs we've collected lately are truly flame chubs, or merely young of the related creek chub (Semotilus atromaculatus). I even woke up first thing this morning worrying about that... now that's bad! But I've resolved my doubts. The confusion stems from the fact that the flame chubs we've collected from two creeks, North Fork of Cypress Creek and Greenbrier Branch, are subadults. They don't show that vivid warm orange on the belly that breeding condition adults do, certainly not at this point in the season. But they do have the red patch at the front of the dorsal fin that is typical of flame chubs, without a black ocellus in it that's typical of creek chubs. The dark lateral line fades out in the caudal peduncle, leaving a dark spot at the base of the caudal. And the general body shape is right, more rotund and compressed looking than creek chubs. So I'm sticking with my official tally of finding flame chubs at 18 of the 47 historic collection sites in north Alabama that I've visited over the last 15 months.

My challenge is to draw up a coherent list of these 47 sites so that Kevin can update the amazing map he's designed for this project. I just now taped up a version that's almost 6 feet long and 3 feet deep, showing the top tier, two counties deep from Tennessee, of north Alabama along the Tennessee River. Most of the historic collection sites are indicated by circles with numbers corresponding to the sequence of sites listed in the University of Alabama Ichthyology Collection records that I'm working from. When I complete my list we can indicate sites that have flame chubs, that don't have flame chubs, or that I haven't been able to visit (yet). The information represented on the map now is that the strong majority of flame chub collections have been made in the Cypress Creek system north and northwest of the city of Florence in Lauderdale County, the northwest corner of the state. With a coherent statement of my data I hope to be able to give a coherent account of the condition of this species in the state. And, of course, you'll read it here first.