Showing posts from September, 2022

Divinity Avenue

I stepped out of the Red Line train at Harvard Square and transited the rest of the way to my destination on foot: 16 Divinity Avenue. It's an awfully grandiose address, but then again, this is one of the places where life's mysteries are discerned. Come to think of it, the group's figurehead even trends toward godlike: he knows a lot of things, shows up in numerous places, and has a lot of power in the community. But even for such a high-and-mighty scientist, he knows who I am. It's one of the reasons I respect him so much.  If you haven't figured it out already, my destination was Pete Girguis's lab at Harvard University. One of my collaborators (Craig McClain) is on sabbatical there right now, and we had a proposal to discuss.  After navigating past the giant mural of the Alvin submersible in Pete's hallway, I found Craig in his third-floor office. We got straight to business: what could reviewers criticize about our proposal? What flaws would we highlig

All that salt

Friends, as you know, I've been working with my grad student lately to try and optimize our methods for extracting and sequencing DNA from larvae. The crux of the problem is that larvae are so small and yield so little DNA that you can't use a lot of the standard methods to check yourself along the way. Basically, you don't know if you've succeeded until the very, very end of the process.  We started with DNA extractions. Then we ran PCRs to copy one particular piece of DNA. It looked like we had succeeded , but then the sequences still came back wonky. It was pretty frustrating.  This is a chromatogram from Sanger sequencing of one of our PCRs. There are supposed to be nice, clean peaks that alternate for the different base pairs, but this is absolute mess.  So I brought in the big guns, aka my collaborator and former postdoc, Hanny. As far as I'm concerned, she knows everything there is to know about DNA , and her insights have kept me sane over the yea

Sitrep: part 2

NOAA divers entering the water at a shipwreck site in Lake Huron. Photo by Stephanie Gandulla. It’s a surprisingly satisfying feeling to watch a field team from afar. Every day, the first email I open is the one labeled “sitrep” – short for “situation report.” That’s the one document that tells me how the field team is doing with their sample collection, and it is so exciting to watch them succeed. Friends, as you know, I’m currently involved in a project that’s testing whether DNA collected from the environment (environmental DNA or eDNA) can be used to locate human remains. eDNA includes everything  – human and non-human sequences alike. We’re not sure if human remains leave a detectable signal in the surrounding water or sediment, so that’s what our study is designed to figure out. My lab is collaborating with the University of Wisconsin Biotechnology Center for the experiment, and we’re funded by the DPAA (Defense POW/MIA Accounting Agency).  Bridget Ladell (UWBC) and Stephanie Gan

The seminar

The opening slide from my seminar Today, I presented a seminar on one line of research I've pursued over the past four years at WHOI. The presentation summarized my efforts as an Assistant Scientist to understand shipwrecks and all of their complex dynamics. I love shipwrecks - you know this, friends. They are large, looming, dynamic, metallic, fascinating, unnatural experiments in ecology. I've dove on shipwrecks in the North Atlantic , tropical Pacific , Caribbean , and Gulf of Mexico , and I can personally attest that each one of them is unique and different.  The challenge for my seminar was coalescing all of my data into a cohesive story. Shipwrecks are diverse, so I highlighted the things they have in common - they're isolated and island-like, they're colonized by invertebrates, and almost all of them have a species that I would not expect to be there.  The sign of a good seminar is the questions it generates from the audience, and I got some great ones. My favori