Mitchell:PCRs, SEMs, Double Helixes and Eight- Legged Wonders | Pinhead Notes From the Field
by Marlee Mitchell
Jul 25, 2007 | 337 views | 0 0 comments | 4 4 recommendations | email to a friend | print
Deoxyribose, a simple construction of carbon and hydrogen molecules, held together by hydrogen bonds to create the double helix that holds the key to all life. Deoxyribose is the basic unit of DNA; when grouped with a phosphate group; Adenine, Guanine, Cytosine, Thymine, it creates the structure we all know so well. Now we can find and sequence this structure using a technique call Polymerase Chain Reaction (PCR) and that is were my trip begins.

With a bumpy start, due to complications with my airline flights, I began my trip to San Francisco where I am currently an intern at the California Academy of Sciences, thanks to the Pinhead Institute, and many others. I am working with arachnid entomologists, Dr. Jeremy Miller and Dr. Charles Griswold in the Entomology Department of The California Academy of Sciences, and this is where my spider odyssey begins. During this internship, I am learning how to use the Critical Point Dyer (preparation for the Scanning Electron Microscope, or SEM), SEM, PCR and Auto Montage (perfectly focused high resolution images). I am also learning basic Arachnid morphology, which is the science of understanding the structures of organisms.

The first week we were introduced to the other interns that are at The Academy and who are also here for the Summer Systematics program which is mostly molecular biology work. We then launched into basic identification of spiders. I also was treated to a tour of the expansive collections found at The Academy. These collections range from jars of snakes to stuffed birds. I happen to think that our insect collection is the best, but it has good competition with the birds of paradise and Native American jewelry and pots. Of course, I have a slight bias. I also learned some basic laboratory technique in pipeting, which is the art of drawing precisely measured quantities of liquids. Being a high school student, I have never used a pipette, nor even seen one, so it was all very informative and a bit difficult, but I think I’ve become proficient at it now!

In order to better understand the collection and its organization, I have been reading literature about the spider families during any free time I have.

Early in my internship experience, we began a “mock” PCR where everything was just water, in order that we could practice. It was very nerve-wracking and it definitely helped to allow me to get used to the pipettes. The next day followed with a real PCR, real experiments where we would be extracting real DNA strands.

In a PCR experiment, there are many different methods and we began by using a method where the DNA is unraveled and then broken apart, this is done a few times. Then all the unimportant debris is washed away and you are left with a clean and pretty sequence. The first process requires us to run a gel. This is done to see if your PCR worked and if you have DNA. You can tell by the bands that appear in the gel when it is examined under an ultraviolet light. To achieve this, we have to use a very nasty chemical called Athenian Bromide. If it touches your skin it will bind to your DNA and basically cause cancer. While using this chemical we use special gloves. The Athenian Bromide is stored securely, however, there are sometimes trace amounts of it on the lab benches. While you are waiting for your gel to set, you may accidentally lean on the counter and become contaminated. How do you remove this chemical from your skin? Strangely enough, the chemical can be de-activated by going out in the sun. So after ever time we’re in that room, I go outside and spin around in the sun, just to make sure. I get the funniest looks, but that’s OK, as long as nothing is binding to my DNA.

After I completed my first PCR, I was told not to expect much. It is very difficult to get good bands in your gel and it takes practice. But my gel showed that I had gotten all bands! My PCR worked and there was a little celebration. My mentor, Jeremy, smiled and said, “Take a good look, because you’re never going to see that again!”

The following days we ran more PCRs and he was correct, as none of the following tests came out the same way.

The next steps of the PCR procedure involves cleaning the PCR and removing all the unnecessary debris so that you are left with nice, clean DNA. I am just now learning this technique.

The lab is OK, but I enjoy the spider identication much better, so I was taught how to measure these organisms. Using a special microscope, Jeremy taught me how to measure the length and width of the abdomen, carapace, sexual organs and all seven sections of the legs. Once I was trained, I was put to work measuring Black Widows from all around the world, from Colorado to Israel. Not all Black Widows have the signature hourglass on their abdomen, with which we associate them.  Many have brightly colored dots or nothing at all. Some do have the hourglass and it is very pronounced.

Through reading I have now established a better vocabulary and I have favorites among these families: the Eresidae family or Velvet spiders, Mimetidae family or Pirate spider which includes the Assassin spider (if you want to find out some strange science, this is worth Googling), and Theridiidae family or Cobweb weaves, which include the Black Widow group.

My Pinhead internship has so far been a whirlwind of amazing information.  I am so grateful that I am here and can’t wait to learn more as there is so much out there to discover in the incredulous world of entomology.

Marlee Mitchell will be a Telluride High School senior this year. She was selected as an outstanding candidate for the Pinhead Internship program and decided to do her internship at San Francisco’s California Academy of Sciences.

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