Processing the Data
Once we return with samples from the field, remember we have those filters full of microbes that we collected from the water, we have to process the samples and isolate the DNA. If you want to read more about field sampling check out my I-Series Journal.
Cracking the Tubes
The first step in processing a sample is to remove the filter (along with all of the microbes) from the plastic container. We do this through a process called "cracking". We literally crack open the tubes with pliers and remove the filter paper. This filter paper is then placed in another tube and stored until we are ready for the extraction process.
Extracting the DNA is a process going through different steps and processes to create conditions that cause the cell to break open are release DNA. We are only interested in the DNA and not any of the other parts so we have to remove the extra junk.
The first thing we do is add some different enzymes to help break up the cell membrane. Each cell is surrounded by a membrane, it is meant to help contain everything, we need to break open that container. So to do this, enzymes help us do some of the work. The membrane is made up of different components and these enzymes (which are just specialized proteins that make reactions happen faster) work to break it open.
We then also go through a process of freezing and rapidly thawing the cells to disrupt them and help break them open. We go from -80ºC in a freezer to 37ºC in the span of just a few seconds.
Our next step involves mixing the cell parts with some different solutions to help separate the DNA from the other stuff. The DNA is much lighter than the other parts of the cell so they start to separate by weight.
Eventually we end up with just the DNA in a little tiny clump in the tube! It's a long process, but careful work leads to easy success. These DNA clumps can then be frozen and sent back to Oregon for further analysis. I wrote a bit about how this analysis takes place when I visited Byron's lab back in May. That journal is found here.
We have to keep everything as sterile as possible to minimize introducing any unwanted bacteria from other environments. We also keep things carefully labeled and organized so that samples are not lost or mixed up.
Today was spent in the lab processing the samples from the I-Series day of sampling. It was cloudy and rained lightly off and on, so I didn't mind staying inside. Once again, I have no new species that I viewed to add to my species journal, but I hope you enjoy this one of a species that does actually live in the area.
Depending on when you are reading this, tomorrow, Friday, June 27th is my LIVE PolarConnect web event. Byron and I will be talking about life at Toolik and in the Arctic, and briefly explaining his research and findings thus far in the study. Tune in! Instructions for registration and access are found here