Student Research at Duke

I haven’t posted much about the progress of the Tomato frog project, but there is lots of good news to report.

I’ve been busy the past two weeks or so with the samples: first isolating DNA from tissue samples (muscle, liver, toes, other unidentifiable body parts), then running PCR on the extracted DNA for a gene in cytochrome b of the mitochondria, and finally sequencing the subsequent PCR product. I received my sequences back from the Sequencing Lab (located conveniently just down the hall in BioSci) at the beginning of the week. I edited the sequences using this pretty awesome program called Sequencher; then I used another fancy program to compare the sequences to each other and also to Tomato frog samples from a previous study.

For various reasons along the way, some samples didn’t work as well as I had hoped. Maybe they were bad samples, maybe the primers didn’t work so well, or maybe I contaminated the samples along the way. (I’m hoping the last reason is not the case, but when a handful sequenced samples register as “Homo sapiens” with the online genome database, I get worried).

So anyways, I started with 36 frog samples and only 12 of them made it all the way through to sequencing. For the 24 other miscreants, the process starts over again: re-sequencing, re-PCRing, and even re-extracting.

I don’t mind all the re-do’s, though, because we got pretty good data from the 12 successful samples. I’ll try to briefly explain what we think we’ve found…

A previous paper looked at two species of Tomato frogs from eastern Madagascar and suggested that the genomes were so similar, maybe these two distinct species shouldn’t be separate at all. Our project looked at ONE species of Tomato frog from various populations in western Madagascar. When we compared the frogs to each other, we found an enormous amount of genetic variation– and after comparing the eastern frogs to the western frogs, we found that there was more variation WITHIN our single western species than there was between the previous paper’s TWO separate eastern species.

So what does this mean? Hopefully, that what we thought was one species located along the western coast is actually two — or even more — distinct species. But of course, we’ll need to sequence the rest of the samples to confirm this.

Anyways, I was pretty excited when I saw what had come out of four weeks of non-stop pipetting. Looks like hard work might actually pay off…

FINALLY, the moment I have been waiting for…the tomato frog samples came in today!!

Alas, they are packaged in a giant cardboard box with hundreds of other reptile and amphibian samples. Maybe “packaged” isn’t quite the best word…apparently throwing all the little tubes in a box and taping it up is adequate for shipping rare frog samples halfway across the world. Shockingly, the box opened mid-trip, and an undetermined number of little tubes may/may not have spilled out.

Anyways, the frogs are here, but first the samples have to be sorted. There are lots and lots and LOTS of tubes. So today, I discovered the tedious side of lab work: sorting and organization. Luckily, everyone tells me I’m anal retentive when it comes to organization, so I seem to have a leg up on this kind of work.

Once the samples are sorted, though, the fun begins…isolating, amplifying, and sequencing the DNA. Lots to do next week!

So I’m starting to see a trend with my lab work…

The past week, I’ve had a LOT of really awesome stuff to do. Sequences, DNA extractions, gels, PCRs, nanodrop machines…tons of cool things to try out. Except for the fact that nothing really seems to work out for me.

I’ll admit, I’m not exactly the amazingly perfect scientist I’d hoped I would be (yet). I don’t really have a natural-born talent to repeatedly pipet single microliters of liquid without fail, and apparently I have some trouble reading directions from a protocol. Like when the book clearly says “add 4 microliters of buffer” and I somehow decide to add 5 microliters. Or when I fail to notice that the vial of DNA-grade water is actually ethanol. Oops. [A note to my lab: don’t worry, I caught my mistakes. Eventually.]

Anyways, I’ve discovered that frequently (and in my case, more often than not) things don’t work out. And sometimes, it’s not because I forgot a step or added the wrong buffer. Thank God.

For example: yesterday, I did a whole-genome amplification on some DNA samples. I managed to follow every single one of the directions, which I thought was a pretty big improvement from my previous week’s performance in the lab. Except that today, I ran out the amplified samples on a gel to gage my success….and I was sorely disappointed. There was almost NOTHING to be seen on that gel.

Luckily, not everything has to be blamed on the scientist (and in this case, that would be me). There is a possibility that it is actually not my wrongdoing at all, and really the horrible amplification is the fault of the company that made the whole-genome amplification kit. At first I thought everyone in the lab was lying and just trying to make me feel better about screwing up so many procedures…but apparently it’s somewhat common for things to just not work out. Unfortunate, but common.

In any case, I’m still crossing my fingers for the shift-blame-from-Sam-to-the-company deal.

A little more information about the Yoder lab…

Basically, all of the research that is conducted in Dr. Yoder’s lab concerns the island of Madagascar. The cool thing about Madagascar is the incredible amount of biodiversity: there are already hundreds of thousands of observed species, and new species are being discovered as I type. The REALLY cool thing is the fact that more than 95% of all these species are endemic and can be found only in Madagascar. Like these cute little guys:

So anyways, everyone in the lab is studying a different Malagasy species to see how they’ve evolved, or how physical barriers (ie rivers, mountains) have affected their evolution. My main project looks at a few different species of Tomato frogs, which are not as cute as mouse lemurs but still pretty funky looking:

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As of right now I’m still waiting for the samples to arrive from Paris, but then I’ll be off isolating, amplifying, and sequencing till my hands fall off from overpipetting.

On a side note, today Steve Goodman came all the way from Madagascar for a visit. According to Dr. Yoder, Steve has done more to study the biota in Madagascar than any living human…and after hearing him speak at the Lemur Center this afternoon, I definitely believe her. He’s spent over 19 years exploring the island and discovering new species. I found this article about him online: “Madagascar Tames the Bohemian of Biology”…he’s had quite a career. I’ve never been to Madagascar and knew absolutely nothing about it until a week ago, but his presentation was great and really makes me want to spend time there myself.

After the speech, the lab and I went on a tour of the Lemur Center (thanks to Aaron, who happened to be at Dr. Goodman’s speech as well). Unfortunately, I forgot my camera today, but hopefully I’ll go back and take some pictures because lemurs are so darn cute. There are some weird kinds though…like the ones with the anal-genital scent glands and therefore rub their butt on every surface to claim their territory. Thank god lemurs and humans evolved differently.

Myth #1: Scientists are crazed workhorses

I mentioned before that I had (still have?) a pretty skewed idea of what “lab life” is like…but today, I realized something monumental: scientists don’t work all the time, 24/7. There IS such a thing as “down time” (thank god!). No one is expected to survive 7 straight hours of micropipetting (unless you have ridiculous forearm muscles).

So to honor my downtime, I snapped some pictures of the Yoder lab. The lab is bright and shiny and brand new; they just relocated this past February. Hopefully I won’t break anything new and expensive in the next eight weeks…

Entrance to the Yoder Lab

a pretty nifty lab bench

the conference room (notice the flowers in the flask…scientists are crafty, too!)

…and my best attempt at a self portrait with some gels

Back to work!