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Cutting-Edge Technologies to Accelerate Plant Research

The Advanced Bioimaging Laboratory at the Donald Danforth Plant Science Center is incorporating machine learning and automation to break new ground in the field of plant science

Lauren Everett

Lauren Everett is the managing editor for Lab Manager. She holds a bachelor's degree in journalism from SUNY New Paltz and has more than a decade of experience in news...

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cell wall components in grass plant structuresSuper-resolution using single-molecule localization microscopy shows cell wall components (white/light-blue foci) in grass plant structures.Credit: Dr. Yunqing Yu and Dr. Elizabeth Kellogg Lab, Donald Danforth Plant Science Center

A facility within the Donald Danforth Plant Science Center (St. Louis, MO) not only has a new name, but also a wealth of new capabilities to drive research discoveries. The Advanced Bioimaging Laboratory (ABL), previously known as the Integrated Microscopy Facility, is incorporating machine learning and automation, as well as state-of-the-art instruments to accelerate the field of plant science.

Kirk J. Czymmek, PhD, who joined ABL as the director in May 2019, has been leading the charge and setting the vision for the facility’s upgrade. Czymmek came to the lab with more than 30 years of advanced microscopy experience. He is an expert in light and electron microscopy, atomic force microscopy, single molecule imaging, super-resolution microscopy, cryo-techniques, and correlative microscopy. As he points out, plant research has been about a decade behind animal research in terms of using the latest technologies available to make new discoveries that can benefit humankind.

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“Keep in mind fungi, bacteria, and viruses are all microscopic, so to understand the basic mechanisms of how these work, you need a microscope. You can see the effects of disease eventually, but if you want to stop it or understand the underlying causes, you will need to magnify it and use special probes and technologies to interrogate,” Czymmek says. That is why he wants to apply new approaches and technologies to plant research at the Danforth Center, but believes the results will improve plant research across the globe. “I’ve heard the expression that St. Louis is the ‘Silicon Valley of plant research’ and it feels true to me. I feel a lot of energy here,” says Czymmek.

The ABL team uses contemporary molecular cytology, preparation, and imaging technologies to better understand the aspects of plant-microbe interactions and fungal cell biology. “Ultimately, our goal is to combine advanced imaging methodologies along with the latest molecular and genomics tool[s] to provide new insights into microbe interactions with plants and their environment to understand the disease-state and promote plant health,” explains Czymmek on the lab’s website.

Catching up

When trying to study plants, unique challenges arise that researchers don’t encounter when working with animal cells. One of the biggest challenges with plants is that they have cell walls that act as rigid barriers, and are often impermeable. Plant cell walls are also made up of different chemicals and carbohydrates, which makes them difficult to analyze, unlike animal cells that have a simple membrane as a barrier. Despite these hurdles, plants have great potential to help improve our environment and educate us on how to maintain a healthy world.

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“When it comes to plant disease, we can’t fall asleep at the wheel and sometimes breeding and genetics isn’t fast enough to stay ahead. We have to find other strategies to prevent disease when it arises, and to understand the fundamentals of how it is caused, which is a lot of what I focus on,” says Czymmek.

Elevating research

ABL is the Danforth Center’s hub for state-of-the-art cellular imaging instrumentation and services. Czymmek utilizes his expertise to help users design and implement their specific imaging experiments. “The number one thing I do when talking to a collaborator is ask ‘what are the scientific questions you are trying to answer?’” says Czymmek. “And then I consider what microscopy tool(s) are most appropriate to help open a door that they weren’t thinking about before.” Just a few months after becoming director of ABL, Czymmek unveiled a suite of new instruments that will further assist researchers in accelerating their projects. One such instrument is the ZEISS AxioZoom microscope, which enables advanced automation to create large area maps and sophisticated multi-location and analysis routines. When asked how ABL has incorporated automation and machine learning into its workflows, Czymmek says, “What I need[ed] is a system that has versatility where it’s not just about taking one picture and walking away from it, it’s about probing the same organism or sample multiple times over a period of time to look at the changes that might be happening to it.”

Donald Danforth Plant Science Center exteriorAn exterior view of the Donald Danforth Plant Science Center, located in St. Louis, MO.Credit: Danforth Plant Science Centerteam of imaging experts and scientists, Donald Danforth Plant Science CenterA team of imaging experts and scientists evaluate the application of single-molecule super-resolution imaging to plant cell wall components with the ZEISS ELYRA 7 microscope. From left to right, Renee Dalrymple (ZEISS super-resolution specialist), Matthew Curtis (ZEISS 3D imaging specialist), Kirk Czymmek (director, Danforth ABL), and Yunqing Yu (postdoctoral associate, Elizabeth Kellogg Lab).Credit: Danforth Plant Science CenterKevin Cox, a Howard Hughes Medical Institute postdoctoral fellowKevin Cox, a Howard Hughes Medical Institute postdoctoral fellow, examines a fluorescent plant specimen using the ZEISS Axio Zoom microscope with Czymmek.Credit: Danforth Plant Science Center

In the fall of 2019, Czymmek also demonstrated the potential of additional technologies the lab intends to implement. One highlight of the demonstration involved the ZEISS Elyra 7, a high-speed 3D and 4D super-resolution microscope that allows researchers to break the diffraction limit using structured illumination microscopy and single molecule localization microscopy techniques using antibodies or fluorescent proteins. This approach creates a two-fold resolution increase compared to traditional fluorescence microscopy, and makes it possible to see the faintest signals and tiniest structures in living and fixed samples.

Another important upcoming addition to ABL will be the Leica EM ICE High-Pressure Freezer—an innovative cryo-preparation approach for light and electron microscopy. As mentioned above, the cell walls of plants create a barrier that makes it difficult to analyze or get probes inside. Traditionally, to resolve this challenge and prepare samples in a lifelike state, samples are immersed in conventional chemical solutions. But during this preparation process, the plant slowly dies, and many changes can take place. “Depending on the biological question you’re going after, using a cryogenic approach where you rapidly freeze the sample and preserve it in a more lifelike state can be highly beneficial,” says Czymmek. This method also allows researchers to handle larger samples. “Previously, we had to cut a sample down to a three-millimeter dimeter size (A = 28.27 mm) and a fair bit of damage can happen to large plant specimens under this constraint. Now we can freeze plant structures that are six millimeters in diameter (A=113.1) with the new design and it is so much easier to use.”

Although this initial expansion of instrumentation and techniques is significant, the ABL team is not stopping there. Czymmek intends to bring even more technologies to the facility, and to update other existing ones.

“Every five years, a major change in optical light microscopy occurs that will change the landscape of how we actually explore plant and animal cells and tissues at a microscopic level. That is why I am pushing for single molecule approaches, super resolution techniques, and techniques where we break the diffraction limit,” says Czymmek.