Extractions

We’ve been processing samples as soon as we collect them in our little Southern outpost lab, making for some very busy days! I could not contain my excitement this morning, so I woke up early, went to the gym, met the team for some breakfast and then we headed off to the lab to extract us some nucleic acids! I started with some RNA extractions using a Trizol-based protocol on paleomats we found buried upslope of Lake Vida in the haltingly beautiful Victoria Valley. We placed the tubes directly into a liquid nitrogen primed cryoshipper in the field, which immediately froze them to -190°C. As we began to process them, the tubes containing the samples turned many shades of pink! The RNA is currently precipitating in absolute ethanol in the -80°C. And of course, we’re also extracting DNA from the same site. Because of variation in lysis and extraction efficiencies of different methods on different types of cells, we’ve been evaluating the relative efficiencies of four different methods protocols (good ol’ Phenol-chloroform, MoBio’s PowerSoil Kit, MP Biomedical’s Ancient DNA Kit, and an Omega Biotek Metagenomics Kit (custom built with our input for extremely long fragment lengths). We’re also testing for differences between lysozyme and a blend of multiple lytic enzymes (aka “polyzyme”) for methods making use of enzymatic cell lysis. So why are we testing so many methods? Because these microbes are known to be difficult to DNA from, if you get any at all. These puppies can be tough to crack open! We quantified the DNA on the Qubit and Agilent to tell us more about the quality of the DNA we’ve extracted. We’ll be using this information to select samples to sequence.

Eventually, we walked out into a beautiful sunlit night to get some sleep. We’ve got sampling to do tomorrow!

DSC_1794Figure 1: Grabbing samples out of the -80.

DSC_1839Figure 2: Lots of tubes!

DSC_2877Figure 3: Angela checking the protocol.