The collections with formalin-fixed samples at Natural History Museum of Los Angeles County. Credit: Shannon Brown
My name is Ryan Moinazad, and this summer I had the incredible opportunity to join NOAA’s Ocean Molecular Ecology group as an undergraduate research volunteer. I’m a rising sophomore at the University of Southern California, double majoring in Biological Sciences and Legal Studies, and I also assist with research at the Natural History Museum of Los Angeles County (NHMLAC). My summer project, a continuation of my work at NHMLAC, focused on a long-standing challenge in science: how to get usable DNA out of specimens preserved in formalin.
Formalin, a diluted form of formaldehyde, has been widely used for specimen preservation because of how well it preserves their shape and form. Museum collections across the world have historically used formalin to preserve samples. The tradeoff is that while formalin preserves the physical structure of specimens exceptionally well, it often degrades their DNA. This damage makes it extremely difficult to recover genetic material, rendering many otherwise valuable collections challenging, or even impossible, to use for molecular research.
Recent research has shown promising ways to recover usable DNA from vertebrate specimens stored in formalin. My project extended this work to formalin-preserved plankton samples collected during the 2020 Washington Ocean Acidification Center (WOAC) cruises using net tows, a common method that involves dragging fine-meshed nets through the water to collect small, planktonic organisms.I compared two different methods for extracting DNA. The key difference in the methods was the chemical lysis solution used to break open the specimens' cells and release their DNA. For each method, samples were removed from their formalin fixation, washed, filtered, and then blended to create an evenly mixed sample. I found that a gentler buffer, closer to neutral pH, extracted ten times more DNA than a stronger, more basic buffer. After extraction, the DNA was treated with an enzyme-based “repair kit” that helps reverse some of the chemical changes caused by formalin.
The next step, which will continue this fall, is to sequence the extracted DNA. Traditional species counts have already been completed for each net tow sample, so comparing the genetic data to these visual identifications will provide a more comprehensive picture of plankton diversity and abundance. This comparison will also help validate the effectiveness of DNA extraction methods for formalin-preserved samples.
Overall, my time with the OME group has been incredibly impactful in both allowing me to grow my skills in research and better understand the invaluable work that happens at NOAA overall. The team here is truly incredible, and I’m grateful for the opportunity to contribute to work that could help unlock the genetic secrets of decades-old marine archives.