About Samantha Kummerer

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Katelynn Koskie #IAmScience

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Katelynn Koskie, a Ph.D candidate, works in Mannie Liscum’s lab. | Photo by Samantha Kummerer, Bond LSC

By Samantha Kummerer | Bond LSC

“#IAmScience because I want to help unravel the mysteries of nature that will improve our futures and positively impact our planet.”

Katelynn Koskie didn’t always know she loved plants. As an undergraduate, she focused on what was above her rather than what grew below her.

“I was really interested in how galaxies interact and then I started to think, ‘you know I’ve always thought plants were really, really cool,’ and I wanted something that was a little bit more down to earth,” she said.

While she was pursuing a degree in astrophysics, she took one plant biology course and fell in love. From there she signed up for grad school and has been with plants ever since.

Koskie works with a mutated plant called hyper phototrophic hypocotyl, hph. The mutation is a variation of the lab’s model plant Arabidopsis. This variation is special. It produces more seeds, bends more under light and is stronger. It’s up to Koskie to figure out why.

That answer could have a large impact on the agriculture industry. If Koskie’s findings can be applied to crop plants like maize, farmers can grow better crops.

“Maize is more complicated than Arabidopsis, but with new techniques like CRISPR/CAS9 now it might make it a little bit easier,” she said.

She plants genetically modified seeds and then waits and observes and begins again.

It is a lot of time in the growth chamber and in the dark room, hoping the research may reveal a breakthrough.

Weighty science

Metabolomics center delves into the unknown

Emily Kummerfeld | Bond LSC

What do you do when you have an unknown substance and need to know what it’s made of? Or what if you know what’s in it, just not how much?

Scientists turn to metabolomics to figure out what these pieces are.

Lloyd W. Sumner, Director of the Metabolomics Center at MU’s Bond Life Sciences Center, said analyzing a sample is like going to the doctor and having blood drawn to assess what’s happening inside of your body.

“Plants can’t tell us what’s going on, animals can’t do that either, so we need high resolution biochemical phenotyping to understand how organisms respond to stress and disease. Instead of profiling one, five, 10 or 30 compounds, we’re profiling hundreds to thousands of metabolites, and we use that to assess the biochemical phenotype and how the system is responding,” Dr. Sumner explained.

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Lloyd Sumner, biochemistry professor and Director of the Metabolomics Center at Bond LSC. | photo by Morgan McOlash, Bond LSC

This is achieved using methods called chromatography and mass spectrometry. These methods separate and analyze hundreds to thousands of metabolites to better understand the biochemistry of living organisms. Metabolites are the molecules a cell creates that provide the building blocks and energy sources enabling a plant or animal to grow, reproduce and respond to its environment. These small molecules can tell us a lot about an organism.

So how exactly how does mass spectrometry work? It really is the science of weighing molecules. It can identify small molecules, quantify known compounds and reveal structural and chemical properties. Crime shows on TV employ the technique in forensic investigations to analyze the molecular composition of unknown substances found at a crime scene.

Let’s break down the process for you.

The first step is actually chromatography, where the molecules in a mixture are separated based on chemical properties. This helps to see individual metabolites within complex mixtures from plants, animals and microbes. Two of the most common types are gas and liquid chromatography. Sumner’s lab uses both since some molecules cannot be heated during gas chromatography and need to be separated via liquid chromatography.

In gas chromatography, a sample is heated until it vaporizes and then travels through a thin glass tube and interacts with a coating on the tube wall. These interactions vary and help separate all the sample’s parts. The speed at which each separate molecule travels helps us determine the identity of each part.

Here’s where the mass spectrometer takes over. As each small molecule/metabolite exits the chromatography column, it enters through the inlet system, and passes through an ionization system that puts a charge on the molecules, since a mass spectrometer does not weigh actual mass but rather the mass-to-charge ratio of the molecular ions. Once the ions are formed, they go through the mass analyzer, which will tell the ions apart based on their mass to charge ratio. From there, the ions hit a detector where a resultant current is measured. This gives scientists a graph of sorts, showing a series of peaks for each substance, with higher peaks indicating more of the molecule in a sample.

This data from both chromatography and the mass spectrometer is then used to figure out exactly what was in the unknown sample.

Control is the name of the game when it comes to getting accurate results. The system keeps samples in a vacuum so molecules can move around without colliding with other gas molecules, because bad things can happen when they do.

“They can deflect the trajectory of the ions as they’re moving through the instrument, there can be charge loss and neutralization of that, but ultimately all of those affect sensitivity,” Sumner said.

Depending on what Sumner’s team is trying to figure out, other types of mass analyzers can come into play. From quadrapole mass analyzers to magnetic sector instruments, to time-of-flight analyzers, they separate the ions in different ways.

Not all mass analyzers are equal as Dr. Sumner explained, “these different types of mass spectrometers have different performance metrics. And as resolution and sensitivity go up, usually cost does, too. But for the most part, we use mostly TOF (time-of-flight) analyzers because they have good mass resolution and the cost is kind of modest.”

The way a time-of-flight analyzer separates ions is actually quite simple. A burst of ions is emitted and accelerated, and the ions are measured based on their flight time over a specific distance, meaning the smaller and lighter the ion, the faster it will be, with each molecule having a unique time-of-flight.

So how does Dr. Sumner use mass spectrometry in his own research? Currently, his work focuses on plant biochemistry.

“We’re trying to understand how plants synthesize triterpenoids. These are important plant compounds that plants use them to defend themselves. They can’t get up and run away, so they make these defense-related compounds,” Sumner said.

The Metabolomics Center benefits more researchers than just Sumner’s team.

For example, his center is collaborating with other faculty on an animal stress test for milk. That’s because the technology at the center can be applied widely to science not only here on campus but nationally and internationally.

An added bonus for Sumner is that his center feeds his fascination with sophisticated analytical instrumentation and electronics, or “shiny toys,” since once “you understand how they work, you get a greater appreciation for them,” he says.

Lloyd Sumner is a professor of biochemistry and director of the University of Missouri Metabolomics Center at the Bond Life Sciences Center. The Metabolomics Center, which opened in August of 2016, is one of ten research core facilities at the University of Missouri. Learn more about the center at http://metabolomics.missouri.edu.

 

How one bad seed could take on climate change

By: Samantha Kummerer | Bond LSC

It’s no secret that the 21st century continues to set records with the warmest years in earth’s history and rising carbon dioxide and sea levels. These significant changes threaten the planet’s future and already challenge farmers.

Mannie Liscum, a Bond LSC investigator, said research in his lab may help address these problems.

They accidentally came across a variation of a plant that reveals multiple adaptive traits, including early flowering

“A variant that flowers early and has other advantageous traits could be very useful because that variant could be grown in more northern latitudes where the day length is shorter than in Missouri, but temperatures are rising to allow its optimal growth,” Liscum explained of the possible implications of the mutant discovery.

Liscum is referencing a shift in temperatures across the world due to climate change.

“We’re seeing broader swaths of the earth undergoing long periods of drought, so we’re getting less arable land, less agriculturally productive land, as we see temperatures rise,” explained Liscum.

These shifts are turning longstanding agriculture norms on their head. Northern U.S. areas are becoming more suitable for growing, while southern regions become less.

Plants designed and adapted to grow in a certain region over decades are suddenly becoming less suited for their region. If you suddenly have to grow corn at higher latitudes with less daylight, the timing of harvest is thrown off. This is because light and temperature affect when plants flower. A shift away from optimal growth regions will increase the time it takes to grow a crop.

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Katelynn Koskie, a PhD canidate, waters young Arabidopsis plants. Koskie studies what causes changes to a plant mutation called hph. | Photo by Samantha Kummerer, Bond LSC

The mutant Liscum’s lab discovered is also more tolerant to drought, produces more seeds, and has a larger biomass. These attributes could lead to increasing crop and biofuel production.

“Any one of those traits, if it actually translates into a crop could be a really big deal,” Liscum said.

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PhD student Johanna Morrow holds up a dish of three-day-old genetically modfied Arabidopsis seedlings. Morrow studies how Arabidopsis responds to light. | Photo by Samantha Kummerer, Bond LSC

How is a plant like this possible?

Researchers are still trying to determine the precise mechanism.

They found this mutation in a model plant, Arabidopsis . Arabidopsis is a simple weed that scientists use to test hypotheses due to its fast growth cycle and their extensive knowledge about its DNA.

Now, to determine if crop plants like corn or soybeans will behave similarly to Arabidopsis, researchers need to understand the mechanism behind these improved characteristics.

The science behind it

This mutation is called hph, hyper phototrophic hypocotyl. The mutation is connected with how plants perceive and interpret light cues.

“Just like we have photoreceptors in our eyes to interpret light cues, plants have different photoreceptors that can sense different qualities and intensities of light, so they can tell high energy or low energy light and that can direct their growth and development patterns,” explained Johanna Morrow, a member of Liscum’s lab.

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Johanna Morrow uses a tool to collect samples of leaf tissue. Morrow will use the DNA from the samples to genotype the plant. | Photo by Samantha Kummerer, Bond LSC.

In the model plant, these photoreceptors fall into several classes, one of which are the phototropins that are utilized to sense direction and intensity of blue light to optimize photosynthesis.

These phototropins play a big role in how a plant interprets light and how it develops. If they were altered or removed, it has a significant impact.

If you remove the phototropins from the genone the plant loses fitness. When grown in the field, one of the fitness consequences of a plant lacking phototropins is increased drought sensitivity. This results in mutants lacking phototropins making less biomass and seed,” Liscum elaborated.

Liscum explained the phototropin sees the light and initiates developmental functions, similar to how an eyeball sees something and then connects it to the brain that then tells your body to move.

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Johanna Morrow collects her samples of leaf tissues from liguid nitrogen so she can extract their DNA. Morrow gathered the samples from plants in the lab’s growth chamber. | Photo by Samantha Kummerer, Bond LSC

Some phototropin can still take in light or “see” but can’t pass the signal properly to the “brain.” Liscum says this is how the hph mutation affects phototropin – he calls it a ‘bad’ copy of the phototropin. Past experiments revealed plants with two bad copies developed worse while plants with two good copies developed better.

However, the best development came from a plant that had one copy of the bad and one copy of the good, as present in the hph mutant.

“When we found this mutation we expected this plant would be blind, functionally blind because it couldn’t interpret the perceived light signal,” Liscum said.

It turned out a plant with one copy of a broken phototropin and one normally functioning phototropin actually developed better than a plant with two functioning phototropin.

“You would expect if you have a bad copy and a good copy you would get worse, not better,” Liscum said.

The lab is still working to determine why the hph mutant does better rather than worse, than a normal plant, but that doesn’t stop Liscum from envisioning the ways this mutant could help the industry.

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Katelynn Koskie finishes planting a new batch of genetically modified seeds. Koskie hopes her experiment can be applied to advancing soybeans. | Photo by Samantha Kummerer, Bond LSC

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A member of Liscum’s lab, Katelynn Koskie, pours a jello-like substance into a dish to plant new plants. The substance allows the plants to stands in place by giving the roots something to grow in. | Photo by Samantha Kummerer, Bond LSC

Considering the potential effect on the genetically modified plant industry, Liscum explained this method would not have any negative side effects to humans because the modification is already naturally found in the plant.

“This would be literally putting a gene that’s normally present in a plant back into the plant but putting a copy in that, on its own, isn’t functional, so it’s not like you’re creating a monster. You’re putting a piece of DNA in that’s normally there but, only you’re using a dysfunctional version in of what’s normally there,” Liscum said.

The hopes are high for the agronomic impacts, but the transfer of the mutant to crop plants won’t be simple.

Katelynn Koskie, a PhD candidate, who is working on applying hph to soybeans, explained soybeans are more complex than the model plant because they have more phototropins.

While more complex, it is not impossible and the team is hopeful.

Experiments begin soon on soybeans and corn and Liscum said he hopes the lab will have answers in the next year.

Mannie Liscum is a professor in Biological Sciences at the University of Missouri. He is also a member of MU’s Interdisciplinary Plant Group that explores new ideas in plant biology. His lab in the Bond LSC studies plants’ response to light on multiple levels and the potential agronomic impact.  

A photo worth a field of change

By: Samantha Kummerer | Bond LSC 

When you bite into corn-on-the-cob or a burger you probably aren’t thinking about what tiny compounds are entering your body or about how they can be improved.

But scientists are.

Those tiny compounds are amino acids and serve as the building blocks of protein. They also play a major role in a recent interdisciplinary research project at the Bond Life Science Center.

Look no further than crops like corn and soybeans. While widely eaten by both livestock and people worldwide, these plants are deficient in several essential amino acids and it takes a lot for the consumer to be satisfied. Amino acids make up a large portion of human’s cells, muscles, and tissues. They are also an important part of nutrition.

“So what do you do in order to get what you need? You eat more, right?” said Ruthie Angelovici, a Bond LSC scientist. “That’s a very big problem.”

Angelovici said the solution lies in learning to manipulate amino acids to improve the quality of the seed.

Previous experiments to improve a crop’s level of amino acid have not had much success, so Angelovici decided it was time to try something different.

She decided ask if different appearances across plants, like the size of leaves or color, have any connection based on the seed it grew from.

Past research suggested that the same genes may control both seed nutrition and aspects like structure, but Angelovici’s research is unique in its combination of research on plant structural characteristics, DNA polymorphism and metabolism. A competitive seed grant of $99,690 from Bond LSC helped get this work off the ground.

She decided a few new tools and people were needed to explore this.

Learning a new language

That’s where Heather Hunt from the College of Engineering and Scott Givan in the MU Informatics Research Core Facility come in.

While Hunt has a background in bioengineering, for years she has teamed up on projects in the Plant Sciences department.

“There’s a lot of things we do as engineers that can be very useful particularly to people in plant science, particularly in terms of equipment and instrumentation, helping them develop faster methods to do things,” Hunt said.

High throughput phenotyping is one of those things. This catalogues a large number of physical features from a study group.

The team determined the research required the rapid collecting of this characteristic data from a large number of plants and multiple levels of analysis. To achieve this, the team envisioned the construction of a physical cart along with the development of hardware and software.

Hunt explained, in the past, students from a bioengineering capstone class would work on a project like this, but the teams kept running into the same problem.

“They were all talented and dedicated and hardworking but there were just things they didn’t know because they weren’t a computer engineer or a computer scientist, so they knew how to code but they didn’t necessarily have the breadth of skills someone in that area would,” Hunt explained of her past project experience.

This time an interdisciplinary team made up of undergraduates in mechanical, biological and computer engineering combined to figure out if a plant’s physical characteristics hint at the content of its seeds.

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MU engineering undergraduates, Jacob Gajewski, Yen On Chan, Nurhidayatun Anuar, and Chloe Rees, stand besides a mobile phenotyping station they designed and built. | Photo by Samantha Kummerer, Bond LSC.

The team spent the last semester building a high throughput phenotyping station costing more than $10,000 from scratch. The station is on wheels can easily be moved between growth chambers. Equipped with cameras, the device photographs eight plants at once. The images capture the plant color, leaf size, and shape along with other characteristics in seconds.

But the road to this final product came with some communication challenges caused by the multiple educational backgrounds of each team member.

“Sometimes we’d have conversations where we’re talking about one thing and we’re trying to all find the phrasing that makes sense to us and we kind of just go around in a circle and then we eventually figure it out, but we get there in the end,” Hunt explained.

Both Angelovici and Hunt said when working in an interdisciplinary team, it is very similar to having to learn a new language.

“As a biologist, I think it’s very interesting to look at how engineers are thinking on things, so working with Heather, for me, was illuminating. We work very differently, we have different languages of how we think about an experiment,” Angelovici said.

Despite minor communication barriers, Hunt said the project has gone unusually smooth for her and credits the interdisciplinary team and the in-depth planning.

“All this interdisciplinary work will be our future in biology, so I think this is a great start for them and for us,” Angelovici agreed.

What’s next?

Now that the station is built, the team is taking the summer to work out kinks and begin initial data collection.

While they hope to one day evaluate crops, the current work is with multiple the model plant, Arabidopsis thaliana.

Data collection for the mock experiment is expected to start late summer. When it does, the team will take photos of many, many plants throughout their four-week life span. The images will then be analyzed for things like the shape of the leaf, the area of the rosette, color, and plant size.

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A look inside the mobile cart the team of engineering students designed and built. The machine photographs eight plants at once using four different cameras. | Photo by Samantha Kummerer. Bond LSC.

“If you can determine the amino acid content in the seed and there’s a specific physical trait of the plant that it portrays, then you can tend to look at a plant and say ‘ok that comes from the bad seed,’” said bioengineering student Jacob Gajewski. “They can then modify it to where they only grow plants with the good phenotypes.”

By December, Angelovici hopes to determine if there is a connection between what the plants look like and the quality of the seeds.

If that connection is established, the next step is to figure out how the two are correlated and if the research and hypothesis are translatable to crops.

This seed funding is one of seven awarded this year at the Bond Life Sciences Center. These awards, which range from $40,000 to $100,000 in funding, foster inter-laboratory collaboration and make possible the development of pilot projects.

 

Ruthie Angelovici is an assistant professor in the Division of Biological Sciences, and is a researcher at Bond Life Sciences Center. She received her degrees in plant science from institutions in Israel — her B.S. and M.S. from Tel Aviv University, and her Ph.D. from the Weizmann Institute of Science in Rehovot. She was a postdoctoral fellow at the Weizmann Institute and at Michigan State University, and has been at MU since fall of 2015.

 Heather Hunt is an assistant professor in the bioengineering Department at the University of Missouri. She earned her B.S. from Iowa State University and M.S. along with her Ph. D from the California Institute of Technology. She was awarded the 2010-2011 WiSE Merit Award for Excellence in Postdoctoral Research and the 2015 3M Non-tenured Faculty Award for her current biosensors research at Mizzou.

 Scott Givan is the associate director of MU’s Informatics Research Core Facility. He earned his B.S. in biochemistry from Purdue University and his Ph. D in biology from the University of Oregon.