Continuing lab work!

I sure miss my 7th graders! (And my family, just in case you're reading this.) Tuesdays in Fort Collins, CO are a lot more quiet than Tuesdays at Brody.

Anyway, Jenny and I showed up in the morning and the blood was gone!  Well, not really but the tubes were now mostly clear since the proteins were broken down.  Now the DNA was floating free from the cells but we first needed to get rid of the proteins.  To do this we added a precipitation solution that caused the proteins to settle to the bottom of the tube after we mixed it up (vortexing) and spun it back down (centrifuging).  The vortex has the purple lid and the centrifuge has a gray lid:

Since the proteins are now at the bottom of the tubes we needed to draw off the liquid which contains the DNA.  This required much pipetting to transfer the liquid to a new tube without touching the proteins at the bottom!  These are pipettes (or pipettors, depending on who you are talking to) and they are used to transfer an accurate amount of a liquid from one place to another.  Because you don't want to cross contaminate your different solutions (and mix up the DNA from one individual with another) you have to change tips (the yellow things) every time!

 

This row of machines are different thermal cyclers that all do the same thing - they replicate the part of the DNA that we're interested in through a process called Polymerase Chain Reaction (PCR).  It's interesting because you put in your samples primers that an enzyme reacts with to copy the part you are interested in many, many, MANY times and the machine heats the sample up to certain temperatures that allow this reaction to take place.

Now that we had the parts of the DNA we were interested in looking at amplified enough that we can actually see them, we now needed to sequence the DNA.  This allowed us to determine the alleles at each of nine microsatellite loci.  Microsatellites are repeating portions of the DNA that you can use as molecular markers to examine genetic information individuals got from their mom and from their dad.  That way I can look and see if an adult male bird is actually the parent of all the chicks in its brood, or if an adult female had multiple fathers of the chicks in her brood.  This is what sequencing looks like using capillary electrophoresis and displayed on a computer monitor:

 

And that was the end result!  Now I need to look at each individual and compare adults and chicks, and maybe figure out who the missing parent is.  Here are a couple of other photos of things in the lab like my lab bench:

 

This sweet little machine is able to tell the concentration of DNA in the samples from a teeny, tiny drop!

This innocent-looking pig is actually a SPEAKER and he helped Jenny and I stay sane through the countless hours of moving liquids back and forth from one tube to another.  The Christmas music that blared from his belly helped get us in the holiday spirit as well.

DNA Extractions!

So in our 7th grade classroom we extracted DNA from our cheek cells AND from bananas - all in less than an hour. Well it is a MUCH bigger task to extract DNA from over 300 little tubes of Mountain Plover blood. I showed up on Monday morning to the Fort Collins Science Center with five boxes of tubes of blood:

 In this box I have it arranged so the tube on the left is the adult and the two or three directly to the right are the chicks. Here's what a tube of Mountain Plover blood looks like:

So the first step was the get the blood out of the tubes and put it into a buffer, because the blood is pretty thick and we need to dilute it.

 The next thing we did was to add two other chemicals that help to break down the parts of the cell so we can get at the DNA. We used shampoo in class to do the same thing. You can imagine this took a LONG time since there were over THREE HUNDRED TUBES!

 

When we finally got all of the secondary tubes (the smaller sample of blood with the chemicals to break down the cells) we then put them in incubators overnight. The middle incubator shakes the tubes as well to mix the contents up.

I'm baaaaaaaack...

Hey Everybody,

So I'm temporarily resurrecting this blog for a week so I can tell my 7th Grade students at Brody Middle School (where I'm serving as a resident scientist as part of my NSF GK-12 Fellowship) about my week at the USGS Fort Collins Science Research Center! I'm working with Dr. Sara Oyler-McCance and Jennifer Fike in the Molecular Ecology Laboratory to examine the DNA in blood samples from Mountain Plover chicks and the adult that was looking after them.

On Sunday the 2nd of December I drove the whole way out from Ames, Iowa to Fort Collins, Colorado! The trip is almost 700 miles, most of this through Nebraska. I'd made this exact trip once before with my brother, so I knew what to expect, but it was still a struggle! I'll admit that I had to stop in Nebraska to take a half-hour nap just so I could make it the rest of the way. For those of you that have never driven across central Nebraska, by the Platte River, it is FLAT!

 

I took this picture from an overpass on I-80 - the tallest thing for MILES.

Anyway, the GPS on my phone sent me kind of a round-about way to Fort Collins. Instead of taking the interstate the whole way it had me go through some small towns and state highways through northeast Colorado. I was a little nervous about running into deer in the dark, since there were far fewer cars on these highways than the interstate, but it looked like the trip would be quite a bit faster. One added bonus was that it sent me past the Pawnee National Grasslands, where some of the first research on Mountain Plovers took place.

I couldn't resist taking a photo of the sign, even though it was dark out.

I made it safely to the hotel and checked in at about 9:30 Fort Collins time (Mountain), which is 10:30 Des Moines and Ames (Central). I was pretty tired! Although I was able to talk on the phone and listen to the radio and audiobooks while I drove, over ten hours on the road is a lot by yourself. And I get to do it again in less than a week!

Next post: what to do with the blood!

Isn't it about time?

So I was just going to write about how it's about time for some sort of update but I re-read the title and remembered those old tv ads by the Church of Jesus Christ of Latter-day Saints (a.k.a. the Mormons) and how they were all about spending more time with your family. So instead of blogging about what's been going on with my family I've decided to get my work done so I can spend more time with my family!

Wow, I'm really bad at this...

I really admire folks who keep up with their blogs! Seriously, when I get back to camp (usually at 10pm) all I want to do is eat dinner (but of course I have to cook it first) and crawl into bed! I COULD walk the 30 yards to the schoolhouse to use the dial-up internet and write about my day but that would mean giving up on sleep/watching a movie/preparing for teaching this fall/working on my manuscript from chapter 2 of my thesis/etc. It's hard enough to get up in the morning as it is!

Anyway, since my last post I have:

Spent nearly two weeks with my major professor (from here on out, SJD) during which time it (of course) rained. At least we got to go to town and stay in a motel! (Which translates into like THREE showers!)
Took a 15+ hour train ride to the Twin Cities where I met up with my family and spent an awesome 4th of July weekend with them! Then took another 15+ hour train ride back to MT. Let me tell you, the anticipation on the ride out made it go a lot faster...
Saw A Prairie Home Companion recorded live.
Listened to literally DOZENS of unabridged audiobooks. (I try and get two days out of each, spacing them out with downloaded NPR podcasts but I'm rapidly running out. I'm saving one for the drive back to IA but it's going to be close!)
Enjoyed listening to Baird's Sparrows and Sprague's Pipits singing from my yard. I could do without the constant Western Meadowlark/Horned Lark/Lark Bunting/Vesper Sparrow singing though.
Scratched a mosquito bite so much that the blood ran down my leg.
Personally found 75 Mountain Plover nests. With the 13 that SJD found I'm at 88 but it'll be REALLY hard to hit 90 in the next two weeks. Actually, I'd like to be home two weeks from today (if not sooner) so I have to get back out there and map prairie dog towns! Hatch little plover eggs! Hatch! (Or get eaten, either way I get to go home.)

Time flies

Hard to believe that I've already been out here two weeks! There was an awful lot of chaos in the household prior to departure with D's tonsillectomy and mix-ups with Enterprise and Transportation Services. I almost had a 2009 Ford Edge with 1800 miles on it, instead I ended up with a 1999 Ford Ranger with 50k+:It actually is about perfect for my needs, but I wish the seat was more comfortable! I've already put a thousand+ miles on it and expect to spend many more hours in it.

I've found 27 MOPL nests so far, which is better than usual, especially since I've been stuck in my trailer due to rain the past couple of seasons. More to come but I'm working on rewriting a manuscript and need to have made significant progress before my adviser gets here.

T-minus one month and counting...

Hard to believe that I head back to Montana in less than a month!