Rotating microscope could provide a new window into secrets of
microscopic life

Date:
August 17, 2020
Source:
Stanford University
Summary:
Insights from innovative device could provide a new window into
secrets of microscopic ocean life and their effects on crucial
planetary processes, such as carbon fixation.



FULL STORY ==========================================================================
Like spirits passing between worlds, billions of invisible beings rise to
meet the starlight, then descend into darkness at sunrise. Microscopic plankton's daily journey between the ocean's depths and surface holds
the key to understanding crucial planetary processes, but has remained
largely a mystery until now. A new Stanford-developed rotating microscope, outlined in a study published Aug. 17 in Nature Methods, offers for the
first time a way to track and measure these enigmatic microorganisms'
behaviors and molecular processes as they undertake on their daily
vertical migrations.


========================================================================== "This is a completely new way of studying life in the ocean," said study
first author Deepak Krishnamurthy, a mechanical engineering PhD student
at Stanford.

The innovation could provide a new window into the secret life of
ocean organisms and ecosystems, said study senior author Manu Prakash, associate professor of bioengineering at Stanford. "It opens scientific possibilities we had only dreamed of until now." Oceanic mysteries
On Earth, half of all the conversion of carbon to organic compounds
occurs in the ocean, with plankton doing most of that work. The tiny
creatures' outsized role in this process, known as carbon fixation, and
other important planetary cycles has been hard to study in the ocean's vertically stratified landscape which involves vast depth and time scales.

Conventional approaches to sampling plankton are focused on large
populations of the microorganisms and have typically lacked the resolution
to measure behaviors and processes of individual plankton over ecological scales. As a result, we know very little about microscale biological
and molecular processes in the ocean, such as how plankton sense and
regulate their depth or even how they can remain suspended in the water
column despite having no appendages that aid in mobility.



==========================================================================
"I could attach a tag to a whale and see where it goes, but as things
get smaller and smaller it becomes extremely difficult to know and
understand their native behavior," Prakash said. "How do we get closer
to the native behavior of a microscopic object, and give it the freedom
that it deserves because the ocean is so large a space and extremely
vertically oriented?" To bridge the gap, Prakash and researchers in his
lab developed a vertical tracking microscope based on what they call a "hydrodynamic treadmill." The idea involves a simple yet elegant insight:
a circular geometry provides an infinite water column ring that can be
used to simulate ocean depths. Organisms injected into this fluid-filled circular chamber move about freely as the device tracks them and rotates
to accommodate their motion. A camera feeds full-resolution color images
of the plankton and other microscopic marine critters into a computer
for closed-loop feedback control. The device can also recreate depth characteristics in the ocean, such as light intensity, creating what
the researchers call a "virtual reality environment" for single cells.

The team has deployed the instrument for field testing at Stanford's
Hopkins Marine Station in Monterey, in Puerto Rico and also on a
research vessel off the coast of Hawaii. The innovative microscope has
already revealed various microorganisms' behaviors previously unknown
to science. For example, it exposed in minute detail how larvae of
marine creatures from the Californian coast, such as the bat star, sea
cucumber and Pacific sand dollar employ various methods to move through
the sea, ranging from a steady hover to frequent changes in ciliary beat
and swimming motion or blinks. This could allow scientists to better
understand dispersal properties of these unique organisms in the open
ocean. The device has also revealed the vertical swimming behaviors
of single-celled organisms such as marine dinoflagellates, which could
allow scientists to link these behaviors to ecological phenomena such
as algal blooms.

In Puerto Rico, Krishnamurthy and Prakash were shocked to observe a
diatom, a microorganism with no swimming appendages, repeatedly change
its own density to drop and rise in the water -- a puzzling behavior
that still remains a mystery.

"It's as if someone told you a stone could float and then sink and then
float again," Krishnamurthy said.



========================================================================== Bringing the ocean to the lab Prakash credit the device's success to the interdisciplinary nature of his lab's team, which includes electrical, mechanical and optical engineers, as well as computer scientists,
physicists, cell biologists, ecologists and biochemists. The team is
working to extend the microscope's capabilities further by virtually
mapping all aspects of the physical parameters that an organism
experiences as it dives into depths of the ocean, including environmental
and chemical cues and hydrostatic pressure.

"To truly understand biological processes at play in the ocean at smallest length scales, we are excited to both bring a piece of the ocean to the
lab, and simultaneously bring a little piece of the lab to the ocean,"
said Prakash.

Prakash is also a senior fellow at the Stanford Woods Institute for the Environment; a member of Bio-X, the Maternal & Child Health Research
Institute and the Wu Tsai Neurosciences Institute; a faculty fellow at
the Howard Hughes Medical Institute; and an investigator at the Chan
Zuckerberg Biohub.

Study co-authors include Hongquan Li, a graduate student in electrical engineering; Franc,ois Benoit du Rey, and Pierre Cambournac, former
summer interns in the Prakash lab from E'cole Polytechnique; Ethan Li,
a graduate student in bioengineering and Adam Larson, a postdoctoral
research fellow in bioengineering.

Portions of the technology described here are part of a pending U.S
patent.

Funding provided by a Bio-X Bowes and SIGF fellowships, the National
Science Foundation, the Gordon and Betty Moore Foundation, the HHMI
Faculty Fellows Program.


========================================================================== Story Source: Materials provided by Stanford_University. Original written
by Rob Jordan.

Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Deepak Krishnamurthy, Hongquan Li, Franc,ois Benoit du Rey, Pierre
Cambournac, Adam G. Larson, Ethan Li, Manu Prakash. Scale-free
vertical tracking microscopy. Nature Methods, 2020; DOI:
10.1038/s41592-020-0924-7 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200817132333.htm

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