Prakash demonstrated the Gravity Machine, which looks like a transparent wheel, in the bustling Physiology course lab, wearing dark jeans and a T-shirt that proclaimed ɫƵExperiment Fail Learn Repeat.ɫƵ
ɫƵThe idea is, if you take a long tube and join the two ends together, it creates an infinite loop of waterɫƵ to simulate ocean-scale distances, Prakash said. Inside the machineɫƵs circular fluidic chamber was Woods Hole seawater, sampled from a boat that morning, carrying all kinds of marine microbes that displayed on the microscopeɫƵs video monitor.
ɫƵNow hereɫƵs a special cell, a dinoflagellate,ɫƵ he said, pointing at the screen at a descending cell. He locked it into the microscopeɫƵs field of view. As the cell moved down, the wheel spun up, and as the cell moved up, the wheel spun down, powered by a machine-learning code tracking an individual organism.
ɫƵIn the frame of reference of the lab, the cell is stationary. In its own frame of reference, it's sinking forever or rising forever,ɫƵ Prakash said. ɫƵSo we've been able to essentially create an ɫƵocean on a tabletopɫƵ using this framework.ɫƵ
Linking Cell Physiology, Behavior, and Ecology
The only constant in the ocean is gravity, while all other conditions ɫƵ light, temperature, pressure, etc. ɫƵshift as organisms move up or down in the water column. Accordingly, they constantly read cues from their environment to make behavioral decisions, such as diving or feeding.
The latest version of the Gravity Machine includes a ɫƵvirtual reality arenaɫƵ where environmental parameters can be adjusted, such as light to dark, specific temperature and pressure - to gauge how organisms integrate these environmental cues to pattern their behaviors.
With the Physiology course students, Prakash used the Gravity Machine to perturb seawater and create ɫƵmarine snowɫƵ: tiny clumps of living and dead microorganisms and other particles stuck together, which sink like little snowballs in the ocean. The students adjusted various parameters, such as water temperature and acidity (which are rising as the climate warms) and observed how the marine snow first forms and its final fate as it sinks to the bottom, capturing carbon.
ɫƵThe rate at which the snow goes down gives us, directly, the carbon sequestration rate,ɫƵ Prakash said. ɫƵAnd that's the worry that we don't understand. How would biology react to environmental change to change this carbon sequestration process? And what is the tipping point? If this sequestration process stops any moment, it is estimated that the CO2 in the atmosphere will instantaneously jump from 400 parts per million to 600 parts per million. But we have no understanding of this, from the perspective of cellular physiology. We know the process works, but we don't know why or how it works and how it would react to climate change. So the big thing we're trying to do is build a map of that.ɫƵ
Prakash much appreciates the ɫƵliving labɫƵ that the MBL provides. ɫƵWe are studying a real ecosystem as close to possible,ɫƵ he said. ɫƵWe go out on an MBL boat every day at 10:30 a.m. and bring fresh samples to the lab from a nearby bloom we spotted on satellites in the morning. Then we organize all the samples by lunch time, so we can do the perturbations that are naturally happening -- temperature, pH, adding microplastics, anything literally that we care about studying.ɫƵ
ɫƵThat gives you a sense of why we are at MBL: physically having this infrastructure and a boat ready to go any time,ɫƵ he said. ɫƵWe sample at different time points, even at night.ɫƵ
In other collaborations, the Prakash lab has brought the Gravity Machine aboard seagoing research vessels, participating in 17 expeditions so far in regions from the Arctic to Antarctica, the Pacific and Atlantic Oceans.
ɫƵIn a lot of cell biology and biology and general, weɫƵve forgotten about ecology in some sense,ɫƵ Prakash said. ɫƵMolecular biology and ecology sort of split apart, 50 or 60 years ago. That was a big mistake. We cannot understand either of them in isolation.ɫƵ
Tracking Marine Larvae
The Gravity Machine isnɫƵt limited to observing single cells. It can also track the multicellular planktonic phase of larval marine invertebrates, when they are too weak to swim and are just carried by tides and currents.
The Prakash lab has measured larval shape, posture, orientation, and feeding and swimming behaviors for numerous marine species, including the purple sea urchin (S. purpuratus), acorn worm (S. californicum), bat star (P. miniata), and sea snails (Credidula sp.) (See Krishnamurthy et al., , 2020). The lab has run expeditions across the world since 2020, and the current behavioral database includes roughly 600 species collected across the planet.
In the future, by adding various modules to the microscope using the Gravity Machine, ɫƵwe foresee measurements that directly link any planktonic cellɫƵs physiological state, such as the phase of cell cycle, to its virtual depth in the water column,ɫƵ the team writes.
Very much in line with the Physiology course ethos, Prakash reaffirmed the need to build new tools to tackle the big unknowns.
ɫƵTools are an incredibly important aspect of thinking about what is possible and what you can actually do,ɫƵ he said. ɫƵIf you donɫƵt make new tools, you canɫƵt ask new questions.ɫƵ