The last day...

Today is the last day of the 2010 DNA Residency. Yesterday we had a "Family Night" where we presented in front of family and friends. There was tons of greek food and the presentations were phenomenal. 

Today, though, we went to an exit interview, cleaned the upstairs loft, went to an hour long lab meeting, cleaned up our bench space, and tried to hide the card we made Kevin, Erica, and Shannon.

We also took a final stop at the Sue gift shop to take advantage of our 20% discount. We got... amazing T-Shirts.

We are truly going to miss this place. It was a wonderful experience that has truly inspired us all.

Thank you Shannon, Kevin, and especially Erica, for making these six weeks unforgettable.

A Deep Dark Secret Revealed....

July 26, 2010 marks the day a shameful weight was lifted off the shoulders of two unsuspecting subjects.

Let me recollect the day's events...

It was just a normal day of work. There was a bit of down time as Claire was waiting for her team members and I, Aileen, was just updating the blog. Many of the other interns were faced with free time so we all gathered in the break room loft. As the minutes passed, we found ourselves playing Family Feud online. Again and again, we answered with great skill to the many categories they threw at us-- but, there was one category in particular that caught my attention. The category was "Which detectives make spy work look like fun", and immediately my mind focused on one detective in particular, but I wouldn't dare say her name.

Throughout my life I have carried a secret. If you have ever been shamefully enamored with something, you can understand where I am coming from. Lurking within the depths of my being, I have been trying to hide that I am an addict- a Nancy Drew computer game addict. With a few exceptions, I have never found a person that shares a passion for Nancy Drew mysteries tantamount to mine. That was until today.

While chilling out in the loft, we were talking about our massive skill in playing Family Feud when my companion and fellow Nancy Drew-er texted me about the latest game- Nancy Drew and the Trail of the Twister. At that point I, very casually and without an overabundance of emotion, asked if anyone had ever played the Nancy Drew games. Thats when it happened.

Claire, a DNA intern who was sitting across from me, responded by saying "I have all of them", and my response..... "So do I". At that point Claire fell to her knees and, with a high pitched squeal, screamed and lunged forward, expelling all of her repressed emotions she had contained over the years. For what seemed like an eternity, Claire clutched my sweatshirt feverishly as we both relished that special moment.

Between fits of constant laughter Claire declared, "I've never met anyone who has played all of the games". The significance of our mutual love for Nancy Drew did not just mark a common interest, but also taught us a lesson. Although differences are obvious, there are and always will be more that pushes us together than pulls us apart.

...Yet another life lesson learned at the DNA Disco.

And When There is Free Time...

We do this.

Or on some occasions, this...

But mostly we do this...

A Visit to the Shedd

Yesterday, some of the DNA Disco interns and other interns working in the Field went on a “behind-the-scenes” tour of the Shedd Aquarium. The normally over-crowded museum was much calmer when we were taken above the exhibit tanks to the opening of the pools where the divers enter. We were able to go up close and personal with animals like zebra sharks, butterfly fish, a gigantic catfish, and the most endangered iguana in the world. Some of the most memorable moments happened when our tour guide fed a tank full of trout who jumped wildly and ended up splashing all the interns or when everyone got scared as the 80 pound catfish unexpectedly made a loud noise as it engulfed a treat .

My favorite moment during the tour happened at the very end. We walked toward a white tank, the tour guide pulled the top off, stuck a long stick in the tank, and pulled out a bright orange octopus. We were all able to touch the octopus, being careful near his tentacles. The octopus had great suction strength, and when our hands touched his tentacles they would stay there until we managed to break away from the suction cups on the octopus. Although physically working with animals is exciting, I would much rather spend my time working on their DNA.

Boy, Do I have a story for You!...

A "Sequence" of Events

Story by: Aileen Nolan

When you have finished your PCRs and checked it with a gel, you are finally ready to analyze on the 3730. A warm fuzzy feeling arises as you finish analyzing and take out that nifty flash drive carrying all the information, a result of all your tedious lab work. You try to hide your smile with your sleeve, as you know that you might hold information that can break your research project wide open. So you take that pretty pink flash drive, you plug it into the computer specifically for the “GeneMapper” program, and finally wait for the peaks on your microsatellite to show. Your eyes scan each chart for the important peaks of the LIZ500 at 139, 150, and 160. Like an ocean wave finally crashing to the sand floor, relief breaks across your face when you see the GeneMapper program correctly measured the peaks.

Next, you begin the laborious work of recording the allele locations. One by one, you record the number on the chart corresponding with the highest peaks... Yes it’s boring, but you know that it will all be worth it when you finally decipher the data. You go dye by dye-- each dye corresponding to a different locus that was analyzed- you record the necessary information. On to the next dye, you continue your records until you notice that many of your samples have no peaks-more than half ….

Well, that’s fine, you reassure yourself. On to the next dye and locus. You go about recording the peaks as usual, but wait, there are none! No peaks at all! Next sample, none again. Next…. none, nada, zilch. Your brows furrow and unnaturally deep wrinkles start forming atop your forehead. That look of calm across your face soon turns into one resembling the look you give when you’ve realized that you’ll never know if Leonardo DiCaprio is actually insane at the end of Shutter Island. All that hard work, capping the strip tubes, aliquoting DNA, running the thermocycler…… all of that needs to be redone.

Finally, you sigh, accept defeat, and trudge onward. Tomorrow will be a new day, and you will sequence yet again in hopes that the machine that costs a quarter million dollars will actually work….. (I kid, I kid).

Which came first?

Being an intern in the DNA Residency doesn't just mean experimenting with different primers or pipetting into PCR tubes all day. Our six week program is filled with more than just lab work--we get the whole nine yards. From lectures to tours to... taking apart eggs?

Two days ago the interns and educators of the DNA residency participated in an embryology lab. The lab, led by John Literacki and Dr. Bill Strausberger, looked at different chicken embryos and their various stages of development. It takes a chick 21 days of incubation to fully develop, so we looked at eggs that ranged from 2 days to 20. In this lab we cracked open the eggs with the embryos that had not hatched but rather died during development. We then cleaned them up and compared the different eggs that had incubated and developed over varying periods of time. My (Aileen) egg was an embryo that was almost fully developed. The chick was physically identifiable and had fully developed features like a beak, webbed feet, wings, and eyes. Some of the other participants' embryos were just a speck, a tiny body with gigantic eyes, or somewhat developed. The dissection itself was pretty gross in my opinion. However, the learning experience was well worth it as it gave a better understanding of not only chicken embryos but also the gestation period and development of all earth's creatures.

After the lab, most of the interns were pretty grossed out and claimed they wouldn't eat eggs for a while. Lucky for them, the next day we were offered delicious breakfast burritos... Filled with, can you guess?

Delicious scrambled eggs!

PCR Troubles

Troubles with PCR is nothing new to the interns working in the DNA Disco center. Team Venom was notorious for having contamination. Gel after gel would reveal that their PCRs were contaminated with some unknown source. A possible reason for why their contamination was so frequent was that their venom gland tissue samples were somewhat old and came pre-contaminated or that their primers were not the good enough quality for their annealing temperature in the PCR process. To try to prevent more contamination they bleached their bench space, changed to filtered tips, sterilized their pipettes, and switched their reagents. Since it is extremely difficult to pinpoint what caused the contamination, some untrustworthy feelings arose amongst the venom team. As a result of their numerous precautions, the problem of contamination has simmered down. However, for our team some problems were just coming to the surface.

Today we were ran gels of DNA from two separate genes and the gels revealed a conundrum. No bands on the gel image showed up. The bands represent the presence of DNA in the PCR samples and when no bands are visible, that means that there was human error during the process of PCR.

What a normal gel image should look like:

All bands are bright and visible, ladders (far left) showed up clearly, blank (circled in black) is empty, meaning no contamination.

What our faulty gel images look like:

Only ladders appear, no DNA bands visible.

The most plausible explanation for this absence of bands is that we forgot a reagent in the master mix of the PCR. We found this puzzling as we had not one but two different PCR's with this problem. Tomorrow we will be redoing these faulty PCR's and get feedback from our advisor, Kevin, who has been away at a conference for several days.

Hopefully we can resolve the issue and determine the exact source of our error.

HAPPY BIRTHDAY ERICA!!

In the middle: Birthday girl, Erica, enjoying her cake. Thanks Shannon!

Today the lab celebrated Erica's birthday. Erica is a scientist in the lab, the coordinator of the DNA Discovery Residency, and also an extraordinary person! She helps every intern through this program, answering questions and giving guidance.

HAPPY BIRTHDAY ERICA!!

Carrie taking secret videos... sneaky, sneaky:

Our procedures...

In the Pritzker Laboratory scientists use different variations of procedures to carry out their research. Much of lab work is based off of preference. In the Pritzker Lab, although there are protocols, each individual manipulates the protocol to fit their project based on coherence and validity. A few of the major procedures that most of the scientists in the lab use are PCRs, gels, and sequencing; however, as mentioned before, each team or scientist tweaks the protocol. Thus, we will be showing you the methods we (Team Shark) use to carryout our research.

Lets Begin:

1. The first procedure we do is a PCR or polymerase chain reaction. A PCR is a way to amplify or make millions of copies of a specific gene sequence of DNA, making it much easier to study and analyze later. A PCR only requires a small amount of DNA, so it's very easy to make tons of copies to work with after starting with only a small amount of tissue or blood to extract from.

How to do a PCR:

*NOTE: We did this PCR with DNA that has already been extracted from a shark's fin.

2. The next step is to see if our PCR was successful. For these purposes we run a Hi-melt Agarose gel. We pipette dyed DNA into a gel and run it through an electric current. DNA fragments move through the gel from negative to positive (since DNA is a negatively charged particle). Shorter bands travel farther through the gel while longer bands travel shorter distances. Using ultraviolet light, we can see the DNA on the gel and see if the bands we are looking for appear. If the samples look good, then we're ready for sequencing.

How to run a Hi-melt Gel:

3. Finally, we determine banding patterns using fragment analysis. We add the finished and checked PCR samples to a master mix of LIZ500 which acts as a ladder for comparison and Hi-Di formamide which denatures DNA. We add the samples and master mix to a sequencing plate which is loaded into the 3730, a machine worth a quarter of a million dollars. Once the 3730 is done analyzing, we can pull the data off a computer and begin scoring the data.

That's the overall procedure and goal of Team Shark. It may sound simple (or extremely difficult) but we repeat these same protocols over and over again for many loci. When we run into errors, we sometimes have to repeat everything over again. Working in the Pritzker Lab has truly taught us the importance of patience.

Welcome to the Pritzker Lab!

Depending on who you ask, a cool thing about working in the Pritzker Laboratory is that it is an actual exhibit within the Field Museum. It is referred to as the “fishbowl” because part of the lab, named the DNA Discovery Center or DNA Disco for short, is behind glass with an added exhibition for museum visitors.

Visitors are able to see exactly what goes on in the lab. That means you are able to see frustration on an intern's face when they get contamination, or relief when they have finished pipetting 96 samples into a sequencing tray. Similarly, the museum visitors are able to interact with scientists rather than just the occasional wave. Week days between 11 a.m. and 12 a.m., there is “Talk to the Scientist Hour”, where guests are able to ask scientists any questions on their mind.

A Formal Introduction...

Welcome to “The Life of a DNA Intern” Blog! This blog is dedicated to documenting the experiences of six high school aged interns working in the Pritzker Laboratory at the Field Museum. The Field Museum is located in Chicago, Illinois, on the lakefront near downtown. Residing on the upper level of the museum is the Pritzker Laboratory for Molecular Systematics and Evolution and Daniel F. and Ada L. Rice DNA Discovery Center. In this lab scientists work with the DNA of different organisms to learn about different aspects of their anatomy, evolution, ancestors, or life in general. There are many scientists working on a slew of different organisms, but the interns in the DNA Residency are being split up into three individual projects. Since there are six high school students and three educators we are split up into teams of three, consisting of two students and one teacher. Each group was assigned a central project. One group works with the evolution of different venomous fishes, another with emerging pathogens in birds, and a final group dealing with population trends of lemon sharks. Each of these teams has an advising scientist, who supervises and tackles any of the numerous questions we ask.

To carry out the research for these projects, each teams uses the DNA of their specimens to run a variety of procedures to ultimately sequence the DNA and analyze their results. For example, the shark team will be comparing their fragment analysis results to that of previously collected data of lemon sharks to analyze population trends such as migration patterns.

Another part of this internship is to educate others about our research and how DNA is used to answer questions regarding natural life. Each group of students is using some sort of digital media as an outlet to teach others and spark an interest in science of those who many disregard it altogether. This brings us to why this blog was created. "The Life of a DNA Intern" was created by the shark team to document the experience and research of the interns and to make it readily available to the public.

Hopefully, with this blog we will be able to make the discoveries and novelties of the Pritzker Lab a bit more understandable and attainable for all those who seek it.