Our Coos Bay microclimate treated us to an exemplary last week: classic fog-steeped mornings and breaks for sun around lunch, and just enough flashes of distant lightning to make us all question our sanity at least once. The first two days were our last of research. I spent them trying and failing to gather some supplemental video data, then farting around with diatoms under the confocal. I came to the Von Dassow lab hoping to learn imaging - I can’t credit myself with comprehensive knowledge of anything, of course, but I wield my new skills with glee. Riley put out the last call for data on Wednesday afternoon, then printed the posters in the mysterious poster dimension. And just like that, all of our projects came to a close, wrapped up, for what it’s worth, in 30-odd-inch cardboard tubes. We celebrated with a charcuterie dinner on the big beach and another good old-fashioned frolic. Thursday seemed to pass in a fugue, as we scoured our presence from the labs, sorting, scrubbing, and dumping our last specimens out to rejoin the sea at last. I bid goodbye to our sand dollar children, which have grown into a beautiful cadre of pluteus larvae. Like any good parent, I did not mention to them the <1% chance of survival for planktonic larvae in the ocean. And yesterday, Friday, was our true last hurrah. We held court in an open poster session, and I got to talk chimeras with so many wonderful students and scientists from the station and its associated departments. I’m so proud of my freakish little embryos - of everything I’ve done this summer - of all of us. We all did fantastic. We were researchers! Then began the time of the rising tide, the time of goodbyes. Evening saw us out at Richard Emlet’s house for a potluck, where we ate good seafood and blew some potatoes to kingdom come with a duct-tape shielded PVC cannon. As the light trickled away back on the station, Ethan finally broke out his famous violin and serenaded us with some Romanian folk tunes. It was a fitting sendoff. To Maya, Richard, George, and Erin; to my REU cohort, thank you all so much for showing me the ropes and keeping me alive, for goofing around and being so serious, for answering my questions and questioning my answers, for making this one of the best summers of my life. It is the half moon of August, the small tide. Maybe some things don’t have to change so much. My sister has come down to get me. In an hour I’ll be packed and gone, back up the coast whence I came, out of the fog and into the rest of the year. And then who knows where? Currents are unpredictable things. But whatever happens, this blog now comes to a close. If you have questions about the program, you may contact me through the form below (emailing to [email protected]). If you’d like to hear more REU research stories, my friends’ blogs and those of past summers are available on this website. As for me, this is El signing off for the last time. Dear readers, friends, colleagues, family, thank you for tuning in. Farewell, and fair winds to you all.
0 Comments
We have one more week. My word, that’s crazy. This place, this project, these people, have shaped and bounded my whole life this summer, and now in seven days, I’ll go. It was a hunkered-down week, all of us working to scrape our data into coherent stories on posters. The task felt a threatening one at first - all those diversions, details, rabbit holes, and caveats I’ve been through in my research, a tale as busy and sometimes chaotic as this season has been. Now that I’ve put it together, though, I can step back and fit it all in the span of my arms. I’ve decided to focus on my chimera project for the final poster, rather than the Rho/Ect2 division recordings. I have much less data for this one, only a single frantic week! But I find myself more excited about this idea and result, and it doesn’t hurt that the pictures are pretty. On Saturday, we got the chance to share our research with the visitors to the Charleston Marine Life Center, the aquarium run by OIMB, which is also the new home for the critters we collected from our dredge expedition on Week 5. Everyone held a station with activities and information for the guests. At mine, they got to look through a microscope at dividing sea star embryos; Naia challenged them to sort green crabs; Ethan and Audrey showed them how to extract DNA, and let them touch a nemertean worm. Remember how we went worm-hunting last week? That was why. The next day, a bunch of the summer students, and Ethan, came down with Covid. Fantastic. That leant a nice whiff of paranoia to the week that none of us appreciated. Luckily, Ethan could get his data manipulation done from his room, and no other staff or students caught the plague. I’d like to thank any OIMB dwellers reading this for working to respond fast and protect each other. This could have really, really, stunk, but instead it just stunk a normal amount Tuesday was Indian Independence Day, so as a welcome break from poster work, we went out to celebrate with Shreyaan. By “went out,” I mean that we picked up butter chicken and curry from American Market (highly recommended) and ate it in the bright evening at Bastendorff Beach. Feeling refreshed, we spent a while frolicking on the wrack line, menacing each other with bullwhip kelp. Everyone presented their first poster drafts for feedback the next afternoon. There’s something special in the chance to see a completed project, a real result, emerge from months of work. Tara, in fact, is off presenting her results at a deep sea biology conference in Brazil! I feel like each of us is an ant, hauling home a grain of information to add to the hill. It took us a season to dig it up. It’s not very big, measured against the ocean of things. But it’s ours. I’ll see you again next week, readers, for my last entry of the summer.
But they each have a full complement of chromosomes and division machinery, shelved and unused. And if you happen to make a slide with lots of eggs all lined up together, and if you happen to squish that slide a bit too much, then by random chance, some of those eggs will wind up with their polar body side pressed up against the glass, physically unable to pinch off and throw away one of those extra mini nuclei. Then, instead of resigning itself to its fate, that nucleus can copy and cleave like a normal cell. This is pretty exciting to me. Polar bodies are part of every animal life cycle, but they’re not often studied, and we don’t know much about what they’re capable of, why they go so quietly, and what would happen if they didn’t. And thus began our quest to raise a larva with one of these extra cells incorporated. We’re manipulating the second polar body, which makes a new cell with two identical sets of maternal DNA; previous studies suggest that the first polar body might not work well on its own. All this week, I fussed over little chemical vials, like a real mad scientist, trying to get our anomaly to happen on command. This has yielded a lot of frustration and some really splendid successes. We’ve had our best luck with cytochalasin B, a fungus-derived toxin that prevents cells from changing shape during division. Even so, small differences in the timing of second polar body formation mean that only a few eggs from every trial actually fail to throw away their extra nucleus. Fortunately, we only need a few. On Monday we injected our eggs with a dye that turns green when exposed to UV light, which lets us mark the third cell using the laser on the confocal microscope. Then, with apologies for the poisons and the lasers, we left the embryos to grow in peace, in the dark underneath a pipette box lid. First of all, this process is far too much fun. Second of all, at the end of the week, we gathered up our precious little larvae for their headshots. And behold! How cool is that? An animal like this, with two genomes coexisting (in this case, the zygote’s and the maternal clone) is called a chimera. It’s named for a monster of Greek mythology, a fire-breathing mishmash hybrid of lion, goat, and serpent. We will see no goat heads sprouting from these sea star larvae, but that interests me in and of itself: the contents of the polar body can function just like a whole egg, if you let them. Though, why do they always end up on the one side? Hm… After the month of wrestling that it took to get my non-answer answer out of the previous experiment, I feel ready to stomp, whoop, and holler over this one. I wish I had more time with it. I also wish I had more time with Coos Bay and with my friends and colleagues. I can sense the last weeks rushing in. Time gets funny near endings, like it does near stars. This week was so labby, and so many people have up and vanished - Madison and Randi to sea with a research cruise, Tara to Brazil for a chemosynthesis conference - that we never got very far outside of campus. But on the weekend before, Devin brought Naia, Ethan, Audrey and I along for his salinity testing circuit, through the winding estuarine valleys under the August sun. And on Sunday I went worm-hunting with the nemertean crew, revisiting the Sunset Bay tidepools. And on Wednesday I crafted a chiton shell out of cardboard, entered the annual costumed OIMB Invertebrate Ball, aka the Spineless Soiree, and danced the evening away like the mollusk I am. How does a mollusk dance? Well, mostly, we lie on the floor. Maybe you’d like it, dear readers, if you tried it too. When last I left you, readers, it was Friday evening and lab had just let out. Not thirty minutes after I’d finished writing that entry, all of us - except the nemertean genetics team, who were grappling with a technical crisis - piled into a car and drove two hours down the highway to Eugene, windows down. Why? Why not! We spent the night at Madison’s house, met her precious and perfect dog, and caught the Saturday farmer’s market. On the way home, missing the damp of Coos Bay, we followed Randi and Madison’s directions to a swimming hole with its own waterfall, and passed the late afternoon frolicking. Sunday was considerably more sedentary. We did, however, rouse ourselves enough for an evening of crabbing down at the marina, which netted us three red rock crabs and one Dungeness (but lost us two really big ones, alas, alack). Audrey, Shreyaan and I also went down to the dock earlier in the day to scout it out, and found ourselves enthralled by seal drama. They were all gone by evening, though. Throughout the week, as the summer weather came into full swing, we visited Bastendorff Beach, Maya Watts' house, the local market, and more, spending afternoons and sunsets in the company of trees and friends. The blackberries are fruiting, the twilight is golden, and did you know Maya's yard has a zipline?! Lab work this week was all about data processing. With ten or so large batch videos, I had plenty of zygote divisions to analyze. We’d even verified our protocol with a rerun, checking for problems caused by squished slides and dye concentration. So there I sat in front of my screen, measuring the furrows that separate cells as they cleave apart, and counting successes and failures. Some went fast, some went slow; some batches cleaved happily and some struggled.
We asked: do subtle tweaks to the waves in these cells alter the way they divide? We learned: “Eh, nah.” At least not the way we did it.
Huzzah. Of course, a no answer is still an answer. I did learn what I set out to learn! And maybe our larger question, about what excitable waves do for a dividing cell, would yield yet a more specific answer if approached from another angle, at another time. Whoever makes that effort can hopefully carry on the thread of information I’ve gathered to their own end. So it always goes in research, I guess. But I’ve talked with George, and together we decided that that person will not be me. The three weeks I have left are not enough time to start and see through a whole followup experiment. So to whoever comes after me, good luck! I hope the eggs cooperate and the (sea) stars align! I hope you’ll find use in my successes, but if not that, then at least in my mistakes; and if not that, then at least may it be a good story! As for me, I’ve decided to spend my remaining time here looking into an anomaly that caught my eye in our videos. So long, I’m off to see a man about a chimera… It’s the halfway point of our summer, and we all find ourselves a little flabbergasted at it. How quickly the weeks go by when you love where you are and what you’re doing! Whenever someone brings it up at the table, we make sure to answer them with an enthusiastic collective “Noooo!” This week, with our methods and trajectories settled out, we presented our project plans to our program heads and each other. I loved hearing about what my friends spend their days doing, and how widely varied our projects get, from genetic sequencing at the bench to crab-wrangling on the marsh. I also started a new test on my Patiria eggs: injection with MPGAP (aka RGA3/4, aka ARHGAP11a, don’t you just love cell biology nomenclature?), a molecule that tamps down Rho activity and dampens the waves on the cell surface. We’ve tried turning our amplifier up, now we’ll try turning it down too. Which speakers will crackle with feedback? A cursory review of our data, however, has also revealed plenty of opportunity for troubleshooting. The eggs in our setup seem to have a harder time with division than we expected. Perhaps it’s the season of the year affecting the starfish reproductive cycle, or perhaps it’s because the cells get squished under their slides. Or maybe our fluorescent probe, a glowing protein fragment that we use to light up Rho under the confocal microscope, is giving them trouble. We’ve started adjusting our protocol to get to the bottom of it.. On the subject of getting to the bottom of things, the REUs did something rather awesome this last Saturday. With pants tucked into boots and ginger snacks in our bags, we set sail on the Research Vessel Megalopa for a dredging expedition. From the jetties of the harbor, fogged as always, we followed the seals and common murres out past the edge of the bay, and there we winched down a grab bag to scoop up a sample of seafloor critters. It was a perfect day for dredging, calm on the water so we could crowd around the sorting table like kids at a candy store. 300 feet down, the world grows dim; detritus-feeders and small carnivores reign. We met familiar animals and bizarre ones: neon-red soft corals, twisty basket stars, scaly worms. I can’t imagine what these fellows were thinking, if invertebrates can be said to think. Most of them had probably never seen full sunlight before. It’s amazing to be surrounded with people who all take as much interest as we do in this strange squishy marine world. And it’s easy to forget that our projects take us to far-apart corners of the estuary and the field of biology - when we talk to each other about research, it feels like we’re all on the same path, encountering the same delights and mishaps. That’s science for you!
My research felt a little like that trail this week. Really it’s been as much obstacle as pathway, and only repetition can clear it. But I know I'm getting somewhere. With methods like ours, you can spend a full day on preparation, and only realize the next day that you bungled it severely. I might mishandle the eggs, or pick a bad batch, and not know until it’s too late. Tuesday was particularly vexing, since we switched over to a new batch of RNA. The cell-city is an exhaustive bureaucracy, and this project puts me in the forgery business. The RNA we deliver must be signed in polyadenlyated triplicate, stamped with 7-methylguanosine, et cetera. All kinds of minutiae can change its effectiveness. Our new batch came out much more potent than the stuff we’d been working with before, and on top of that, something seemed fishy about the eggs too. After getting careless with the timing and then rushing to arrange everybody for the camera in proper order, I watched my precious cells rally for division, only to scrunch themselves into the most horrifying popcorn shapes. But we make what we can of it. Every day I still get more comfortable with our tools and familiar with the laws of the microverse, and I begin to accumulate the almighty data. And hey, now we know the proper dosage for our new RNA: On Friday we tried again with our calibrated doses, and got a pretty good run. In lab, not every unexpected development is an unwelcome one. This week I caught a firsthand glimpse of larval metamorphosis as one of Chloe’s subjects, confused, attempted to settle and transform in her dish, pushing its digestive tract out through its side. Another day, while I was injecting and Chloe was filming, George brought his guitar into the scope room, and we learned a sea shanty.
There ought to be a sea shanty written from the perspective of a marine larva. The narrator rides the current, braving storms and monsters; 99% of its original crewmates perish, and when it reaches port at last, it breathes a sigh of relief, turns itself inside out, and becomes a worm. A noble life indeed! This week began in fire - a campfire. We spent Friday evening through Sunday morning at Sunset Bay, trekking the shoreline all day and huddling around the firepit, like hydrothermal vent creatures, late into the night. There Ethan exposed us to the horrors of the highly elaborate pun, Shreyaan had a birthday, and Naia, Audrey and Chloe inaugurated a minor deity (a bag of jalapeño kettle chips). While camping, we once again visited the intertidal, this time at a straight channel worn into the rock, a geology like the splitting edge of an old book's leather spine. Riley, a TA at OIMB and one of our trip leaders, taught me the names of seven or so seaweeds, from iridescent Mazzaella to lumpy Leathesia. We cracked open a sea urchin and scraped out the yellow meat from its hull: uni, the animal’s gonads. Now I’ve eaten invertebrate eggs while studying invertebrate eggs, and I can say with all honesty that they were delicious. By high tide that day we were up above the headland’s cliffs, finding our way from cove to cove through tracts of woodland and meadow. The weather turned bright, just in time, and we could see out to the bar where seals lay watching us. Dandelions and rockweed all day… then back to our fire for the night.
When we watch the cells divide, we’ll have to do so with multiple techniques. Some of our properties of interest can be measured in bulk, from footage under normal light, but some will require close-up images from the confocal microscope, using its laser to visualize dyed features of our cells. This all involves a lot of sitting in side rooms, peering into an eyepiece, with one hand on a precision tool and the other on the microscope controls as I fiddle around with egg cells. I’m sure plenty of people would find this the height of tedium, but I’m sincerely enjoying myself. It reminds me of the middle phase of a drawing, when I trace over my pencil sketch with linework, repeating the details until everything’s complete. As I get used to the tools, I’ve been able to watch myself improve at my procedures. Last week, egg sorting frustrated me, but now I can use the micropipette to pick up individual eggs! And I only kill (with freakish consistency) 11% of the eggs we subject to the microinjector. Under the confocal and its singing tunable crystal - yes, really - the cells glow and squirm as they multiply, doing the dance of embryogenesis before our eyes. Oh, and an update to our sand dollar larvae: they're thriving, fed the finest lab-grown algae twice a week.
We rise early and sleep early at the research station, stepping out in the mornings onto the fog-banked marina. Egrets, cormorants, and pelicans, commuters from across the bay, remind me that the sea has edges. At the start of the day, I like to walk across the bridge and back, or to visit the lookout point we found in the woods.
This week saw the beginnings of our projects. Chloe and I first slopped down onto the mudflats to dig up buried worms - the parents of her larval subject - and antagonize shore crabs; then we harvested sea star eggs and learned to operate the microinjector, which will be one of my main tools. For my project, I want to examine a peculiarity of cell division in sea star eggs. Cell division is a dynamic process, but it relies on a basic series of steps. Imagine that I need to bisect a circle of paper. First, I’d use a ruler and compass to orient myself with the center. Then I'd take a pen and draw a dotted guideline there. Finally, I’d fold and cut along the line. Simple as that. Animal cells, as it turns out, go about things in a similar way, using proteins. They have a folding machinery (called actin, also responsible for muscle contraction), an “inked” guideline (called Rho), a drawing hand (called Ect2), and a compass to direct it (the thready spindle structure of mitosis). But from a protein’s perspective, a cell is not a neat geometry on paper: rather a crowded, whirring industrial city. Just look at this section of the cellular landscape modeled by Evan Ingersoll & Gaël McGill. Down here, there are no straight edges, no convenient blank spaces to draw in, and nobody looking down to guide it all. Our sequence of steps, communicating only by touch, must coordinate with each other to act in synchrony across that entire city. A sea star egg cell measures about a quarter of a millimeter across - large enough for the human eye to see. It is a very big, very busy city, and sometimes the signals, the steps of division, get confused. Yet these first divisions touch off the entire undertaking of animal life. An invertebrate egg, cast out into the sea, must be especially keen to get itself divided and functional. What’s a cell to do? For the past few years, George’s lab has probed the way Ect2, Rho, and actin work together in sea star eggs. By tweaking their sensitivity, we can spark off striking ripples of activity at the cell membrane, causing Rho and actin to assemble and fall apart again in waves. It seems to be an extreme expression of a natural process, a feedback loop built into the cell. But what’s it for? Well, here’s one idea: how about an amplifier to help the machinery of division communicate across a big city?
Rho waves on the surface of a sea star egg with its excitability turned up through excess Ect2 protein. This figure was published in Nature in 2015 ( Bement et al ).
Hopefully, I’ll be able to test this idea in my project this summer. We might take a sea star egg and chemically nudge Ect2 and Rho a little, then watch how the subsequent divisions go. The difficulty lies in catching it on camera… and in doing this without killing them! I wanted to practice on the fertilized eggs of the ochre star, Pisaster, a common sight in the tidepools. But after severely traumatizing nearly a dozen Pisaster specimens (gamete harvest for this species involves lopping off an arm) and finding not a single fertile male, we got fed up. We’ll be using the bat star Patiria miniata for our experiments instead. Expect to see a lot of pictures of Patiria eggs in the coming entries. Lots and lots... Greetings, readers - El here, live from the clinging fogs of Coos Bay. I’m thrilled to be part of the OIMB research community this summer. I come from Seattle, on the Salish Sea, a day’s drive north from here and a kindred ecosystem to this one. Poking around in the intertidal and the fir forest here, I realize I’m doing the same thing I’ve been doing for twenty-odd years: it was by crouching down and poking at invertebrates that I first discovered an interest in biology and art. I currently study Biology at Brown University in Providence, beside the other ocean. The Atlantic is lovely, but the chilly, smelly, alive Northwest Pacific is home to me. I’ve spent this first week getting acquainted with the fellow-creatures, human and otherwise, of OIMB. Last Saturday I moved into the dorm, alongside 10 other REU students. These fantastic people left me no reason to be nervous about meeting my coworkers, even in a building with walls that do not close all the way. We’ve gone out to explore the nearby coast and woods together, discovering secret passages, accumulating convenience store candy, and having narrow misses with toxic newts. We’ve also defeated a truly demonic puzzle. I’ll be lab partners with Chloe Goodsell; we both work under the mentorship of Dr. George von Dassow. George’s lab studies invertebrate embryos and larvae. You may witness the splendor of larval biology yourself by leaving something, maybe something expensive and clean, floating near shore for a month or so. Behold: a colorful community of life appears, seemingly from nowhere.
Cast adrift in a vast and often hostile world, an early larva must somehow form itself into an individual, and gather enough resources to maintain functionality, while surviving its habitat and its neighbors. Luckily, unlike rising college seniors, larvae are shaped by evolution to meet that challenge. I can’t wait to get to know them! George is teaching Chloe and me the tools and techniques to peer into the larval world - microscopy, organism collection, embryo culture. We’ve spent many afternoons getting close and personal with the local plankton. On Monday we also fertilized some sand dollar eggs in a dish, so in a way we’ve already created life. Two days later they’d become spaceship-like pluteus larvae, and we practiced preparing them to film. Even for a kid (me) who used to sort boxes of Cheerios for fun, manipulating individual cell clusters is a challenge. These little guys will grow through the summer, developing as our projects do. As for what the projects are? Tune back in to find out, next week! |
|
Proudly powered by Weebly