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Showing posts from 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

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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 just...an 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

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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

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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

That smooth curve

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"Oh, it's beautiful!" I exclaimed, "look at that smooth curve!"  Beside me, Kharis was just as excited - although not quite as vocal. I pointed at the screen with both hands. A smooth fluorescence curve on the graph indicated that our sample contained DNA. "That means it worked!"  "No, yeah, I get it," Kharis nodded. "Cool." We were upstairs in a colleague's lab, using a fluorometer to measure the concentration and purity of DNA in some samples. Some of you might remember that I've struggled for a few years with methods for extracting DNA from larvae . The problem is that larvae are so small, a single individual doesn't have a lot of DNA. Any of the tried-and-true extraction methods I use for larger organisms don't really work well for larvae because they include wash steps. Of course, washing a sample is meant to carry away everything except the DNA, but a little bit inevitably gets lost with each step. When there

Persistence

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The Meyer-Kaiser lab, summer 2022: Kimberly, Kharis, Kirstin, and Kraken If I had to describe Kimberly in one word, it would be "persistent." Her determination to meet a goal honestly blows my mind. When I said something along those lines to Kimberly's mom today, she got this knowing look in her eyes that only mothers have and nodded, "Yep, that's who Kimberly is."  Kimberly joined my lab this summer through WHOI's internship program, and what a summer it has been. Her project was to analyze images from the Arctic seafloor and track changes in the invertebrate community over time. The project should have been straightforward - count some animals, do some statistics, learn about the Arctic. Or so I thought.  When a medical event forced Kimberly off campus, I honestly thought she would not come back. I even moved her research from my list of "projects underway" back to "future projects" on the whiteboard in my office. But Kimberly persi

The American Blue Economy

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A few weeks ago, I was invited by Admiral Tim Gallaudet to participate as a guest on The American Blue Economy Podcast , which he hosts. If you're not familiar with the concept of the Blue Economy, it refers collectively to activities in the ocean or other major bodies of water like the Great Lakes, which support economic growth, improve livelihoods, and sustain the health of aquatic ecosystems. Admiral Gallaudet has spent his career in the Blue Economy, first as Oceanographer of the Navy, then as acting director of the National Oceanic and Atmospheric Administration (NOAA). He regularly writes op-ed articles with well-informed and articulate positions on the importance of the ocean for the American economy and national defense . It was an incredible honor to be invited on his podcast, and now that the episode has been finalized, I'm excited to share it with you.  The episode I participated in was part of a sub-series called "Women Wavemakers," which highlights the r

Bench work.

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 Believe it or not, I love bench work. That term refers to all the tasks that must be completed at a lab bench - microscopy, molecular biology, measuring concentrations, weighing things, and the list goes on. The past few weeks, I've been standing at my lab bench at least half the day to extract DNA from Porites lobata . PLOB (with a clam in the foreground). Photo by Kharis Schrage. You remember Porites , friends. It's the coral species that my team is  working on in Palau . Matthew, who spent the past several years working on a whole range of species in the Caribbean, uses four-letter abbreviations to refer to species: one letter for the genus and three letters for the species. So Porites lobata becomes PLOB. And you know what, a "plob" is kind of what Porites looks like. I've gotten pretty good at extracting DNA from Porites lobata the past few years. My collaborator, Sarah, calls my methodology "clutch" because the DNA comes out so clean. It's

The nuptial dance of the nereids

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Invertebrates are awesome. In fact, if there was a "moral to the story" for this blog, that could very well be it. Today, I want to share a tale of some particularly awesome invertebrates. Their name is Nereis succinea . Nereid worms, for those of you who have not met them before, are wriggly little beasts. They're polychaetes, which means they're worms with myriad fringes down both sides of their bodies. They typically live in marine sediments and eat whatever they can get their jaws on. Those jaws, by the way, are freaking awesome. When a nereid eats, it everts its pharynx - in other words, it turns its throat inside-out. That pharynx can be surprisingly long, and it is armed with pinching jaws made from protein. I've held a nereid in my hand while it tried to bite me before - trust me, that experience was highly unnerving.  A hopeful Nereis succinea bachelor in my lab. Nereids also have fascinating reproduction, and that is what brought a researcher all the wa

Maritime Heritage Ecology

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Friends, I am proud to introduce you to a new term: Maritime Heritage Ecology .  This phrase refers to the fusion of biology and archaeology that is necessary for understanding the processes that shape underwater cultural heritage. As many of you know, I've studied shipwrecks since my PhD. They're island-like systems that aren't supposed to exist, so they present a number of extremely interesting biological questions. But shipwrecks aren't just habitats - they're also historical and cultural resources. They undergo their own transformations, as wood degrades, fishing gear gets entangled, artifacts get scattered, and metal corrodes. Shipwrecks are incredibly dynamic.  Moreover, shipwrecks are not the only type of cultural heritage that lands in the ocean. There are cars, planes, and tanks. There are structures like lighthouses, wharfs, ancient villages, and middens. There are artifacts like amphoras, statues, and weapons. All of them tell the story of human interacti

Maximize

 "Let me swim against the tide... Maximize me  Let's go beyond reality If you can see what I see Hypnotize Maximize me" - "Maximize" by Amaranthe Every time I have a few spare minutes, I pull out an old project and try to take it one step forward. It's the only way I ever manage to finish things. The project I'm trying to finish now is my "dock study," which some of you might remember from 2017 . I spent the whole summer collecting data on fouling communities with my intern, Nicole , and we found some pretty cool stuff - bryozoan, hydroids, sponges. The project even had a surprise twist at the end when most of our animals died and were replaced by recruiting  barnacles . I started the summer with all sorts of fancy hypotheses about how the species were going to interact in intricate, mechanistic ways, but by the end of the summer, I had come to the conclusion that succession in marine fouling communities happens in one of two ways. Sometimes,

Problem solvers: part 2

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I know I've said this on the blog before: science involves learning all sorts of random skills that a normal person doesn't need. As problems come up , we do whatever it takes to fix them. Here's my latest example.  A Niskin bottle in my lab with both ends open. There are these things called Niskin bottles that are incredibly common in oceanography. Everyone uses them. The bottle itself is made out of thick plastic (PVC), and it has water-tight caps on both ends that close when triggered. You open the bottle on the surface, let ocean water flow through it all the way down, trigger the closing mechanism at your desired depth, and then bring up a sealed, temperature-controlled sample of water from a precise location. Niskin bottles work great.  I bought 10 Niskin bottles for our eDNA project and shipped them to Saipan for Calvin and Evan to use in the field. At the end of the trip, they packed the bottles back in the original boxes, added the padding, and sent them to me. Ea

Non-stop

 "Why do you write like you're running out of time?" - "Non-stop" from the musical Hamilton by Lin-Manuel Miranda Oh, this career is non-stop. Since getting back from the Gulf of Mexico, I have been writing constantly. A scientific study is never finished until it's been published, so sometimes I think I'm actually a professional writer. Here are some of the things I've been working on writing lately:  The Palau paper: The coral samples that Hanny and I collected in Palau in 2018 showed some really cool genetic patterns. In fact, that study is what launched our entire Palau project that's taking place now. It usually takes a while for datasets to get written up, edited, submitted to a journal, reviewed, revised, and finally published. This particular manuscript is in the revision stage, and we're almost done! The reviewers had some substantial comments that we needed to address, but now that we've worked our way through them, the manu

Dragonflies: part 2

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When we got back to land, the first thing I noticed was I noticed was the dragonflies. Once again, they were fluttering around  Sea Scout 's working deck, gracing our world with their iridescence.  M/V Sea Scout at the dock in Louisiana. Photo by Calvin Mires. It felt weird to wake up and find the ship motionless after a week rolling around at sea, but we returned victorious to Intracoastal City, Louisiana. This project is actually a dream for me, because we put in equal effort on the shipwrecks and the hard bottoms. We collected data from seven sites total - four shipwrecks and three natural reefs. Usually, my datasets are either all shipwrecks or make just a passing effort at documenting nearby hard bottoms. This time, I have nearly equal data from both. Moreover, the reefs we looked at were the closest natural hard-bottom sites to each shipwreck. Two of the shipwrecks were equidistant from the same hard bottom, so I can actually do a one-to-one shipwreck-reef comparison. How do

Mystery in the mesophotic

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Our goal for this project was to document three shipwrecks and associated hard-bottom sites - that was the bar for success. By the end of the day on the Hamlet , we had reached that bar, and we still had an extra day at sea. We transited a few miles back toward land and set about investigating a new shipwreck.  Sonar image of the unknown wreck  The mystery wreck looked like a fishing vessel from the sonar. There were doubts that it would be historically significant, but it still represents an important component of the Gulf coast's Blue Economy: fishing. As the ROV descended, we could see the shipwreck's bow come into view on the sonar. The metal V-shape was clear, even through the murky water. As we approached, the organisms living on the wreck came into view. There it was: Tubastraea coccinea , the orange cup coral. Tubastraea coccinea is not native to the Gulf of Mexico. It comes from the Indo-Pacific and has spread across much of the Gulf and Caribbean since its arrival. I

The Hamlet

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Our dives today were focused on a shipwreck named Hamlet . The Norwegian oil tanker MV Hamlet was transporting a load of crude oil from Beaumont, Texas to Liverpool, UK in 1942 when it was struck by a torpedo from the German U-boat U-753 in the Gulf of Mexico. Along with the CP Baker , it's one of the historically-significant wrecks we're investigating - and another one associated with the oil and gas industry. This photo is from a reconnaissance last year, when the visibility was much better. Check out the corals on that gun! The dive on the Hamlet did not go perfectly, I have to admit. For a start, the visibility was horrible . We had actually encountered the "murk layer," as Evan calls it, during our dive on the hard-bottom site earlier that morning. It was impossible to see anything unless it was directly in front of the vehicle. Just brown, turbid soup.  We found the shipwreck thanks to the magic of sonar and approached it from the stern. Of course, we didn'

CP Baker

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Yesterday was an amazing day. We had a little touchy conditions in the morning - swift current, some waves - so we delayed launching the ROV until right after lunch. Once we got in the water, though, oh man, did we find cool stuff.  My sea fan (or black coral?) specimen We started on the hard-bottom site. It was a little knoll in the middle of the mud. We started at the bottom of it and worked our way up the slope, past rocks with crustose coralline algae, encrusting sponges, and sea fans. I'm not actually sure about that last identification - I've been calling it a sea fan, but it might be a black coral. One thing is for sure: it is everywhere. The ROV doesn't have a manipulator arm to collect specimens, so I was starting to disparage my ability to identify the species. As it turns out, no manipulator arm was necessary! The ROV's thruster got some strands stuck in it, so I was able to save the specimen for identification later. I'm excited to do the full analysis b

Wreck and boulder patch

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We have done it! We had a successful dive yesterday and were able to collect data from both a shipwreck and its nearest natural hard-bottom habitat.  Sonar image of the shipwreck and the hard-bottom site. I was the scientist in charge for the hard-bottom site. I sat beside the ROV pilot in the shipping container that serves as their control van on the deck. Radio in hand, I communicated with the navigator up in the lab, the captain on the bridge, and the pilot beside me. We surveyed the site by flying over it with the ROV and collecting video. We really weren't sure from our preliminary sonar data what we were going to find at the hard-bottom site. It just looked rough - it could have been mussels, rocks, or just clumps of mud. It turned out to be basalt boulders that had probably ended up on the seafloor through a geological uplift.  There wasn't a ton of stuff living on the boulders, but then again, we were pretty deep - about 80 m. I noted crustose coralline algae, some oran

Shakedown

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Preparing to deploy the ROV on Sea Scout. The vehicle itself is in the cage, and they're  both lowered over the side with the winch.  In ocean science, we frequently refer to a "shakedown." It means the first attempt at something, when you identify all the problems and get your procedure set. Well, yesterday was our shakedown on the Sea Scout .  The day started with the ROV team and videographers working together to integrate their systems. As I mentioned, the ROV we're using isn't typically used for research, so we added an extra camera for data collection at higher resolution. Whenever you try to integrate systems, there will inevitably be a thousand tiny things that go wrong and have to be addressed, and that was definitely the case yesterday. It took a long time.  My major goal for the day was to get the ROV wet - just put it in the water, I didn't care how deep. We were eventually able to dive in the evening, although that was a shakedown of its own. The

Dragonflies

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My favorite thing about the South is the bugs. No, I'm not talking about the mosquitoes that swarm around your head or the flies whose bites hurt as much as they itch. I'm talking about lepidopterans. I'm talking about coleopterans. I'm talking about arachnids. You know - arthropods. There is such incredible biodiversity in the southern United States.  Dozens of dragonflies flitted around the ship. Their long, needle-thin bodies gleamed and glimmered in the sunlight. A brown-and-white-striped spider darted out from under a box and caught a moth to munch on. A beetle climbed the side of the ship as I ascended the ladder. A large grasshopper rested atop the bow spotlight at dusk.  MV Sea Scout in Amelia, LA. Photo by Calvin Mires. Friends, I am in on board the MV Sea Scout  in rural Louisiana. When we arrived, the ship was unassumingly parked alongside a grassy field in a bayou. It was a rather surprising place to find a ship, if I'm honest. Calvin and I boarded, go

Time series

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It's hard to believe I've already been home from Palau for three weeks. The first week was lost to sleep - ask my husband, I was a lump. The second week was mostly paperwork and digging myself out from under the mountain of things that had accumulated while I was away. And now, here we are.  It is definitely summer. Woods Hole is full of tourists, and all the visiting scientists at the Marine Biological Laboratory down the street from WHOI are noticeable around town with their signature teal lanyards. WHOI has its own summer crowd too, although they're not quite so numerous or conspicuous. I actually have a summer student of my own this year, named Kimberly. She's a Cell and Molecular Biology major at the City University of New York, and she's been wonderful to work with so far.  Kimberly's project is an investigation of temporal patterns in an Arctic deep-sea community. She's actually continuing a project that I worked on back when I lived in Germany 10 yea

Strawberry milkshake: part 2

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My last night in Palau, Cas insisted we go to Bem Ermii. It's the food truck across the bridge in Airai that serves burgers, fries, and milkshakes. He needed a strawberry milkshake , he said, to make sure we got more spawning. After working in the ocean for the last 12 years and monitoring coral spawning over the last month, I have to admit that I understand why sailors are stereotypically so superstitious. Events seem so random sometimes, you try everything you can to gain control. Strawberry milkshake it was.  Maikani "Selfie Queen" Andres got all four of us and the  sunset in a single image. We ate our dinner on the dock and watched the sunset - that was Maikani's idea. It was beautiful. Not just the sunset, but sitting on a boat trailer with my team, passing around the squeeze bottle of mayonnaise, eating in relative silence, just enjoying each other's company and the natural world around us. I needed that time to zoom out and appreciate the moment.  It feels