Category Archives: Lab Work

May the clams be with you

It feels like we just came back from the workshop in Panama. Time has been flying like never before. Is that normal in January? I have spent most of it in the laboratory, extracting DNA from clam gills. Matt introduced me to Gustav Paulay at the Florida Museum of Natural History. Gustav studies biodiversity on coral reefs and Pacific islands. He regularly organizes large-scale taxonomic surveys but he also tests hypotheses about the past census of biodiversity on earth before human activities using paleontological, ecological, and phylogenetic tools. Matt and Gustav have collaborated extensively in the past. I reached out ot Gustav to ask for more lucinid clam gills to complement our collections of closely related host species on both sides of the isthmus. I hit the jackpot! Only a few days after I had returned from Panama, we received a package from Amanda Bemis, Gustav’s collaborator at the museum with very precious clam gills, carefully preserved in ethanol. The extractions went well, hopefully we can start sequencing soon!

Lucinid bivalves from the wet collections of the Florida Museum

I caught fire. Motivated by the kindness of Gustav and Mandy, I reached out to many museums across the country with presumed collections: Oregon State University, the Cal Academy of Sciences, The Natural History Museum of Los Angeles, UC Santa Barbara, Harvard, and eventually also the Smithsonian collections in D.C. Many passionate emails. Most of them responded. Material Transfer Agreements to sign. Bothering Jonathan to be responsible. And many, many more nights in the laboratory extracting DNA from clam gills.

The largest specimen so far!
From a Galapagos expedition more than 50 years ago!








The DNA integrity of our fresh clams from Bocas del Toro in December 2018 is far better than any of the museum specimens stored in 70-100% ethanol. The expensive Zymo buffer did a brilliant job of shielding our DNA. RNAlater looked weak in comparison. Museum specimens resulted in high concentrations but very degraded DNA. However, it looks like some of them will fill some important gaps of sampling with regard to the genomic information of the lucinid chemosymbionts.

While I am writing this, Matt and Jarrod are traveling to Coiba accompanied by a visiting Master student – Jade Sourisse, two interns – Catalina Rodriguez and Helio Quintero, and two expert taxonomists from Brazil – Arthur Anker and Paulo Pachelle. They are taking advantage of extremely low tides during this time of the year. This trip is part of our big effort this year to finalize the collection of samples. They will look for snapping shrimp, sea urchins, reef fish, and lucinid bivalves. Jarrod even contacted Aaron O’Dea who generously offered equipment to dig for sediment with fossils and lucinid bivalves. Oh, I wish I could be there right now!

Check out this video from Wyatt Toure who took their field course on Coiba a few weeks ago!

I am sitting here in Davis and taking a fieldwork safety training and learning how to teach a seminar in marine microbial ecology. After my official transfer to UC Davis, I am taking advantage of the resources that are provided for international expeditions, including survival training, a satellite phone, and international health care. The latter includes free vaccinations and malaria prevention. If everything works out, we will soon travel to Costa Rica and dig for more clams. When I go out in the evening to look at the moon, I think of Matt and Jarrod further down south along the Pacific coastline looking at the same moon. Stay safe on Coiba!

On a brighter note, team Davis is welcoming a new undergraduate researcher, Ipek Yasmin Meric. Yasmin has worked the last two weeks in the lab and helped me dissect clam gills and extract DNA. She also supported me mentally through the more or less useful/necessary/laborious RNA removal treatments and several rounds of running gels and normalizations. It is a pleasure to have her around. We hope to see some sequences soon.

Yasmin dissecting gills from museum specimens.

Meanwhile in California — Porcelain crab collection for an undergrad project

While David and I went on the urchin/crab collection expedition in Panama earlier this year, we had two undergraduate students from UC Davis starting a project in the Eisen group. Amy Wen and Jolie Lobrutto are interested in learning more about the bacteria that are growing inside urchins and porcelain crabs.

Originally, we planned to bring tissues back from Panama for them to dissect and screen for microbes. However, permit issues prohibited this endeavor. Instead, we decided to focus on urchins and crabs in California. Eric Sanford, a collaborator at UC Davis who is a group leader at Bodega Bay and using urchins as a model species provided us a specimen from the lab and another one from the field. Amy and Jolie dissected them while David and I were lost in Panama.

A few weeks ago I teamed up with Jonathon Stillman, a professor at San Francisco State University & UC Berkeley, and an expert on porcelain crab physiology. He had a collection trip scheduled to look for different species of Porcellanidae at Fort Ross. The tides were low and we were able to collect a good assortment of four different species. Amy and Jolie could not join us because the low tide chart coincided with exams. Nonetheless, they could spare some time to come to the lab and culture bacteria from the new specimens. Amy and Jolie are now experts on the culturing of host-associated bacteria. Soon they will learn how to identify the bugs using Sanger sequencing.

Laetitia and Jonathon looking for porcelain crabs at Fort Ross
Jonathon explains how to identify different species in the field.
Laetitia showing California crabs to Amy and Jolie

We are curious to learn more about which bacteria they found on urchins and porcelain crabs in California!