qPCRin’

Today (8/11/14) I showed up bright and early to the School of Aquatic Science and Fisheries at the UW campus in Seattle. I was surprised by how close it was to the NOAA facility. Maybe I shouldn’t have been. Anyway’s after getting the lay of the land and acclimating myself to this very creepy scull (see figure 1). We began work. I focused on extracting Labby DNA. It was pretty straight forward but it was my first time using these kind of pipettes and so it took me a moment to get used to. On the whole the qPCR looked like it turned out great but we are still in the process of interpreting the data. I am very excited to learn more about the data we have collected. Perhaps the most unexpected part of today was how straight forward qPCR is. I was expecting it to be super high tech and very complicated with lots of blinking lights and whizzing machines like something you might see in Dr. Frankenstein’s lab (side note/creative writing idea: would it be cool to be a grad student with him? Also what granting agency do you think he applied to to fund his experiment? If he didn’t have any grad/undergrad students what did he say were the broader impacts of his grant?) anyway all that is to say that the qPCR machine was in fact the exact opposite. It was a very modest little black box with a computer screen connected to it. It worked just like a normal PCR except you didn’t have to run a gel. As I understand it (and it would really help me if someone corrected me where there are apparent gaps) we are using qPCR to quantify the amount of Labby DNA during different points of the replication process of the template DNA. That makes sense to me and I understand how regular PCR that is visualized on a gel doesn’t tell us how much DNA is there only the size of the DNA. But what information about Labby infections in eelgrass can we glean from our qPCR experiments? Why can’t we extract DNA and do a regular PCR and then measure the concentration of the DNA in a NanoDrop Spectrophotometer? Wouldn’t that also theoretically give us an idea of how much DNA results from a PCR? We could even stop the PCR at different points during the run in order to plot multiple points on a graph of PCR product over time.

Fig. 1. Creepy scull found outside Lisa and Carolyn's lab. Perhaps this inspired my creative writing prompts about Dr. Frankenstein.

Fig. 1. Creepy scull found outside Lisa and Carolyn’s lab. Perhaps this inspired my creative writing prompts about Dr. Frankenstein.

A different type of pipette that I have not seen before but have now figured out and am excited to use again at some point in the future.

A different type of pipette that I have not seen before but have now figured out and am excited to use again at some point in the future.

Lisa and Amanda looking at the qPCR output.

Lisa and Amanda looking at the qPCR output.

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