Thursday, July 31, 2008
Wednesday, July 30, 2008
Sunday, July 27, 2008
Tuesday, July 22, 2008
Sunday, July 20, 2008
I found my study plant, Physaria bellii, or Bell's Twinpod, by visiting with the Colorado Natural Heritage Program's very competent botanists and giving them sort of a laundry list of what I wanted in a study system, and they were happy to oblige: I wanted the sites 2 hours or less from my home, I wanted to work with something that at the time of the conversation (September) still had vegetation showing so I could collect leaf samples for DNA, and if possible, something that was rare and hybridizing with a more common congener. But not too rare, as I didn't want to compromise the species by sampling it.
How about Physaria bellii? Okey dokey. Physaria bellii is named after the namer's colleague, which sometimes happens in science. The genus belongs in the Brassicaceae, or mustard family, and P. bellii is just one of several narrowly-distributed species of Physaria in Colorado. It is a habitat specialist, found mostly in soils from the Pierre and Niobrarra shale formations, which make up hogbacks running along the east side of the Front Range of Colorado from Denver north to WY. It will also sometimes be found in soils associated with red sandstone. The habitat is patchily distributed, and as a result, one might hypothesize there is limited gene flow.
In the process of studying this species, I came across a simple table by Deborah Rabinowitz, which is called the Seven Forms of Rarity. When you compare the various combinations of population size (large or small) and geographic range (broad or restricted), there are seven ways a plant species can be rare. You'll notice there's an eighth combination, but that's when the factors come together and the species isn't rare (large population size, broad geographic range).
Here's the table:Physaria bellii comes in at the upper rightmost cell. It's locally abundant in its preferred habitat, but that habitat is rare, so it is as well. Notice how plants can be rare in a variety of ways, and of course this helps when trying to figure out how to conserve rare plants.
OK, a bit about the looks of this plant. As you can see from the picture, it's a low-growing plant, and has yellow flowers. Those flowers smell very nice, as I found out when I was growing them in the greenhouse to do crosses. I guess I had just never bent down close enough in the field to get the scent. They are pollinated by generalist pollinators, and can have 50-200 flowers open at one time. The flowers mature into the "twinpod", a two-part fruit that can have two seeds per side, but usually has one. The leaves are covered by tiny hairs, perhaps as a water-loss-prevention adaptation. The leaves are variable, but all spatulate with no sinuses, and this helps distinguish P. bellii from its relatives.
Next time - hybridization, population genetics and chromosome squashing.
Friday, July 18, 2008
Wednesday, July 16, 2008
If you are interested in science, how many are you qualified for? Here's a few that I qualify for, along with their explanation from the site:
The “talking science” badge. Required for all members. Assumes the recipient conducts himself/herself in such a manner as to talk science whenever he/she gets the chance. Not easily fazed by looks of disinterest from friends or the act of “zoning out” by well intentioned loved ones.
The “cloner” badge. In which the recipient has cloned something or other. Rules to a drinking game concerning this badge will be forthcoming.
The “sexing up science” badge. In which the recipient has had experience with things such as selective breeding, crossing, mate selection, prokaryotic conjugation, fertility studies, STD related microbiology, and/or any other acceptable interpretation of the badge.The “destroyer of quackery” badge. In which the recipient never ever backs down from an argument that pits sound science over quackery.
And there are a couple that I wish I qualified for....
The “I work with way too much radioactivity, and yet still no discernible superpowers yet” badge.…Although not for lack of trying…
The “my degree inadvertently makes me competent in fixing household appliances” badge. Not necessarily a good thing.
I originally saw this on a great blog, "Not Exactly Rocket Science"
Tuesday, July 15, 2008
Now, if my surge protectors/power strips would get here, I can stop playing "what's not being used and can be unplugged?" 7 pieces of equipment and 4 outlets.
Monday, July 14, 2008
Hey, though, I can rise to the challenge. I spent a couple of hours looking over what I had squirreled away, as we have to stock up over the two month ordering freeze that occurs in August and September every year anyway, and came up with an order (actually 5 orders to 5 different companies) for about $4,800 worth of stuff.
Now I am in no danger of running out of PCR or sequencer supplies, and will be able to get back to the lab shortly and get back to work. I also have a hard time getting over how expensive some of the supplies are, with propriety mixes of stuff for the sequencer being the most outrageous.
Sunday, July 13, 2008
I have recently been turned on to TED, which is a collection of videos on a variety of topics, and if you have any extra time, check it out, I don't think you'll be disappointed. I have an interest (not quite sure what to do with it yet, but something will happen with it, I'm sure) in the communication of scientific information to non-scientific people. That's not supposed to sound disingenuous; I hope that by spending time with Mr W looking at ant colonies, he'll choose not to kick them as he goes by (which he did do, once) and instead gain some kind of appreciation for them.
If you follow this link, it's a 20 minute talk on ants by a researcher in SE Arizona, who studies what she calls "task allocation" in harvester ants.
Some fun facts:
A queen can live for 15-20 years.
All ants are colony dwellers
There is no central control - yet the ants work cooperatively
The four tasks in a colony (besides those of the queen) are: foraging, patrolling, maintenance and garbage detail
While ants have eyes, smell is the most important sense
Ants can switch tasks, based on the pattern of antennal contact in other ants they encounter
I still am having trouble figuring out how to embed video, but I'll work on it.
I like the tie-ins of her work to decision making in other areas.
Wednesday, July 9, 2008
This mentor, let's call him Dr. R., started his job as a research geneticist on campus right about the time I started school. We went to hear him speak as part of a plant reproduction class, and I was hooked on the work they were doing and wanted to be a plant geneticist.
I can remember one of our first meetings, where I'm sure it was obvious that I knew hardly anything about population genetics. I nodded, took lots of notes and I think "got" about 50% of what he was saying. After 8 years, I get close to 100%, I'm happy to report, and I'm still taking notes at our meetings. So much so that he commented today, "you are the most prolific note-taker I know!" To which I replied, without a hint of sarcasm (I hope), "well, you say a lot when you talk."
I imagine he's repeated some of the same things several times, but he's walked me through the subtleties of doing the various analyses one does when doing population genetics studies. What are the assumptions of the test you're using, how does this software calculate this metric, how do you interpret this value. There's still a lot to learn, but I continue to be amazed and compelled by the information that can be gleaned from DNA-based data.
The best part? He was saying how he's co-author on a grant by yet another committee member of mine, and I chimed in, "well, my contract is up in a year, so if you need any help, you know where to find me". And, to my surprise (only because money always seems to be too tight to hire new people) he said, "we're trying to get funding to hire a couple more support scientists, so keep your CV current." Sweet!
Tuesday, July 8, 2008
Probably like a lot of places, we can't order supplies or equipment from the end of July until the beginning of October, due to efforts to balance the books at that time. I'll need to inventory my stuff and make sure I have enough to do everything I'm supposed to do.
I did get the specimens' DNA extracted and PCR'd yesterday, and will check the PCR products on an agarose gel today. Then I'll run the PCR product through a kit that cleans out the unwanted reagents and use another kit to introduce the PCR fragments into bacterial vectors, as I begin the process of cloning and sequencing these fragments.
In other news, I'm finally meeting with someone to deal with my tree lawn, which looks horrible, as I have herbicided the grass and stopped watering. I just can't do the digging myself, so I'm taking bids from a couple of companies to install RR ties around the edge of the tree lawn, and I'll buy and haul mulch to cover it all up. It will be nice not to cringe a little every time I look at it.
Monday, July 7, 2008
We're looking for evidence of hybridization between two species, P and R, that aren't supposed to hybridize.
Although we are starting with a region of ribosomal DNA, my feeling is that we'll need to look at other markers as well. Some specimens, morphologically, have looked "funny" to my boss, but he ID'd those as R. I can remember when he made his comment a couple of years ago, and of course my first question was, "do P and R ever hybridize?" At the time, he said, emphatically, "no". Then we found several instances, then several instances more once we started looking for them, of individuals who showed both diagnostic bands for both species on our species-level screening PCR.
So the plan is to sequence the ribosomal DNA of 5 individuals that showed both bands and that had their morphology examined by an expert (my boss). 3 were ID'd morphologically as P, and 2 as R. We'll run our panel of microsatellite markers on them as well. I did a small sample (1 per family, 48 families) of R, just to see what their microsatellite profiles would look like. I got about 20% with P profiles.
It's a cool conundrum. Stay tuned.
Sunday, July 6, 2008
I had to think about it, but I finally came up with 17:
Bowling Green, OH: 7
Norwalk, OH: 1
Fremont, OH: 1
Toledo, OH: 1
Fort Collins, CO: 5
I moved yearly when I was going to school for my undergrad, followed by the first round of grad school. Then there were several years of moving around when I was married, trying to find a place where we could live and both have jobs.
I've been in CO now for 11 years, this house for almost 3. Moving so often (well, it feel like it's been pretty often) has made me less of a pack rat than I think I would have been otherwise. Before every move I've gone through my things and made the "Goodwill pile" of items to give away.
My current house is by far my favorite, for lots of reasons. It's mine, for one, and I LOVE the area. I already know that it won't be the last place, though. At some point CB and I will get a place that will have to be larger than my little cottage. And when that time comes, I'll have my tape, boxes and Sharpie marker at the ready to get the job done.