For the past two weeks Amanda and Shawn have been busy in the lab prepping and conducting their experiments and today they would find out if they were successful. They left the field a couple of days ahead of us so that they could get a head start on cleaning, melting, and filtering almost 300lbs of the ice that we collected. It was all in an effort to extract the microorganisms out of the ice so that they could isolate the ATP, DNA, and RNA in their cells. Today Amanda would find out if she isolated the RNA and Shawn would find out if he had ATP.
All of our lab benches were covered in filtering materials, glassware, PCR machines, and everything else that we would need to conduct our experiments.
Remember that two of the important questions that our research is meant to answer are: Are the microorganisms that we find in the glacial ice alive and are they metabolically active? For Amanda's experiment she is taking RNA out of the cells of the microorganisms that we find in the ice. This is important because the DNA that we find after filtering can come from living or dead microorganisms, but RNA degrades much faster and if we find RNA in a sample it usually means that the organisms were alive. After she isolates the RNA she is going to amplify the 16s gene in the ribosomal RNA. All bacteria have this gene and by sequencing it and looking at the small differences you can actually use it to identify specific species of bacteria. If she gets enough RNA, she can use a kit to convert it back to DNA and take it home safely for sequencing. It's pretty cool stuff. After a couple of long days and nights in the lab, Amanda got her results and they were great. She managed to collect 3 times more RNA than she can usually collect and she was able to identify and amplify a portion of the 16s gene and convert it back to DNA. After all the stress, she definitely had a successful day.
Amanda is conducting one of several steps to extract the RNA out of the bacteria cells.
Amanda's experiment was a success. The red arrow points to her control and the yellow arrow points to her RNA. Yeah she got RNA!!!
Shawn also had a successful day. After two tries he managed to extract the ATP out of the cells and quantify it. All cells have ATP because it is the molecule that they use for energy. We know that every bacteria cell has about 2 X 10^-18 mol of ATP. If we quantify the amount of ATP in an ice sample and then divide by that number we should be able to tell how many bacteria are in our sample.
After melting and filtering the dirty ice we were left with a pile of smelly mud that Shawn formed into a ball.