Drowning in Data

New web-based framework helps scientists analyze and integrate data

By Emily Kummerfeld | Bond LSC

Large-scale data analysis on computers is not exactly what comes to mind when thinking about biological research.

But these days, the potential benefit of work done in the lab or the field depends on them. That’s because often research doesn’t focus on a single biological process, but must be viewed within the context of other processes.

Known as multi-omics, this particular field of study seeks to draw a clearer picture of dynamic biological interactions from gigantic amounts of data. But, how exactly can scientists suitably weave multiple streams of information together, especially considering technology limits and other biological variables?

Trupti Joshi and her team are seeking to find a solution to that problem.

Joshi, as part of the Interdisciplinary Plant Group faculty, works on translational bioinformatics to develop a web-based framework that can analyze large multi-omics data sets, appropriately entitled “Knowledge Base Commons” or KBCommons for short. She describes KBCommons as “a universal, comprehensive web resource for studying everything from genomics data including gene and protein expression, all the way to metabolites and phenotypes.”

Her work began about eight years ago with soybeans. Dubbed the Soybean Knowledge Base (SoyKB), her team had developed a lot of their own data analysis tools for soybean research, but they realized the same tools could help research of other organisms. From there sprouted the Knowledge Base Commons, intended for looking at plants, animals, crops or disease datasets without the need to “reinvent the wheel” each time.

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Soybean plants used in research that utilizes Soy KB web-based network. | Emily Kummerfeld, Bond LSC

“Our main focus has been in enabling translational genomics research and applications from a biological user’s perspective, and so our development has been providing graphic visualization tools,” Joshi said.

Those tools provide an array of colorful graphics from basic bar graphs to assorted colored pie charts to help the researcher better analyze the data once data has been added to the KBCommons.

Colorful graphs and comparisons lets many researchers look past the lines of text and tables full of numbers that represent genes, plant traits or other experimental results, and making the interpretation of data much more easier and efficient.

One particular tool allows the researcher to look at the differential genes of four different comparisons or samples at the same time. Differential genes are the genes in a cell responding differently between different experimental conditions. For example, a blood cell and a skin cell both have the same DNA, however, some genes are not expressed in the blood cell that are expressed in the skin cell. With this KBCommons tool, a researcher can examine genes to see “what are the common ones, what are the unique ones to that, and at the same time look at the list of the genes and their functions directly on the website, without having to really go and pull these from different websites or be working with Excel sheets,” Joshi explained.

She envisions KBCommons as a tool to enable translational research as well. Users will be able to compare crops, such as legumes and maize for food security studies, or link research between veterinary medicine and human clinical studies for better therapies.

Intended for a wide range of users, Joshi is keenly aware of its potential users right here at MU.

One current user of the Soybean Knowledge Base (SoyKB) system is Gary Stacey, whose lab at Bond Life Sciences Center studies soybean genomics and to date has been the longest user of the SoyKB resource. Like many researchers, Stacey explained the need for a program like SoyKB that can process enormous amounts of data.

“The reason it’s called “Knowledge Base” is the idea that we’re putting information in, and what we hope to get out is knowledge. Because information is different than knowledge,” he said, “we don’t just want to collect stamps, we want to be able to actually make some sense out of it…By having a place to store the data, and then more importantly have a place to analyze it and integrate it, it allows us to ask better questions.”

This is essential, given that one soybean genome is 1.15 GB in size, and one thousand soybean genome sequences could generate 30 to 50 TB of raw sequencing data and tens of millions of genomic variations (SNPs).

But such numbers are modest compared to the program’s true capabilities.

“The KBCommons system is so powerful that it can allow you to run thousands of genomes at the same time using our XSEDE gateway allocations,” Joshi said. “This whole scalability is a unique feature of KBCommons, which a lot of databases do not provide, and we are happy we have been able to bring that to our MU Faculty collaborators on these projects, so that they can really utilize the remote high performance computing (HPC), cloud storage and new evolving techniques in the field.”

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KB Commons is a new web-based network for biological data analysis and integration developed by students. | Emily Kummerfeld, Bond LSC

Mass data capability and colorful graphs aside, her favorite part is who exactly is designing the program.

“What I like most about KBCommons is that it serves as a training and development ground and is developed by students, undergraduate and graduate students from computer science and our MUII informatics program.”

KBCommons is still under development, but publication and access for all users is planned for the end of this year or early 2018. Users will not only be able to view public data sets, but add their own private data sets and establish collaborative groups to share data.

Dr. Trupti Joshi is an Assistant Professor and faculty in the Department of Health Management Informatics, the Director for Translational Bioinformatics with the School of Medicine, and Core Faculty of the MU Informatics Institute and Department of Computer Science and the Interdisciplinary Plant Group.

 

Striking Oil

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Jay Thelen, a Bond LSC researcher, next to the GC-MS machine in his lab, which tracks seed oil measurements. | photo by Mary Jane Rogers, Bond LSC

How to get crops to produce seeds with more oil

By: MJ Rogers, Bond LSC

You can’t get blood out of a stone, but Jay Thelen wants to find ways to get more oil from seeds.

“We’re specifically working on the metabolic engineering of oil seeds. Broadly, trying to increase the oil content of crops and raise the value of the seed in the process,” said Thelen, a Bond Life Sciences Center researcher.

Seed biology and metabolic engineering have long been interests for Thelen, and his lab combines biochemistry with cutting-edge proteomics technology to identify new regulatory modules for key metabolic enzymes.

But let’s start with why seed oil is important.

Seed oil is big business, enough so that scientists are trying to maximize the amount of oil that seeds produce. It represents an important, renewable source of food and feedstocks, used for everything from salad dressing to combustible fuel. More than 448 million tons of oilseed crops were consumed in 2015-2016, according to USDA Economic Research Service.

The oil essentially comes from lipids, or fats, in plant seeds or fruits. All plant cells contain lipids, and embryonic cells within young seeds are poised to make an abundance of them, especially the storage lipid triacylglycerol.

While tree nuts can be up to 80 percent oil, most oilseed crops store 15 to 45 percent oil within their seed. Through biotechnology and metabolic engineering scientists want to increased this amount, something Thelen aims to do.

His end goal is to increase the oil in crops such as soybeans and canola, but any biotechnological idea for increasing seed oil starts in the model plant Arabidopsis.

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Modified plants that are being grown in Thelen’s lab in Bond LSC. | photo by Mary Jane Rogers, Bond LSC

“Arabidopsis is easy to transform in the lab and has a short life cycle,” he said. “We can use this plant to quickly demonstrate proof-of-principle for enhancing seed oil and then advance successful strategies to soybean, camelina, or canola.”

To increase seed oil content, Thelen’s lab works on a large protein complex called Acetyl-CoA carboxylase or ACCase – an enzyme that catalyzes the first step towards oil production.

“We made a recent breakthrough on the regulation of this complex,” Thelen said.

The proteins critical to this process are called BADC proteins – they are kin to an essential part of ACCase, but are inactive. BADC proteins significantly inhibit the activity of ACCase by mimicking its functional sibling and slowing the complex down.

Basically, BADC is a way for the plant to control and slow down the production of fatty acids. By “turning off” the BADC protein, ACCase is de-regulated and oil content in seeds significantly increases.

“We leveraged this discovery to make higher oil producing plants by simply shutting down expression of this gene family by RNA interference,” said Thelen. “Consequently this increased seed oil content quite a bit. We’re now in the process of studying gene knockouts for this family in soybean and camelina.”

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Yajin Ye, a postdoctoral researcher from China, adds water to the plants in Thelen’s lab. | photo by Mary Jane Rogers, Bond LSC

Yajin Ye, a postdoctoral researcher from China in Thelen’s lab, is in the thick of this work. He spends his time modifying seeds to maximize seed oil content and tracking the seed oil measurements in the GC-MS instrument.

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The GC-MS machine, which tracks the seed oil measurements. | photo by Mary Jane Rogers, Bond LSC

“If you want to know how much oil is in each seed, you use this instrument,” Ye said, pointing to the GC-MS. “It measures the oil content of the samples we provide it.”

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Arabidopsis is a model plant used in Thelen’s lab and the seeds are much smaller than most people would expect. | photo by Mary Jane Rogers, Bond LSC

Arabidopsis seed are much smaller than most people expect, so tiny and light that researchers have to be cautious that they don’t become airborne and cause cross-contamination. In addition, soybean plants are kept upstairs in a fifth floor greenhouse at Bond LSC. While camelina are grown in growth chambers within Schweitzer Hall as part of a collaboration with Dr. Abraham Koo, an assistant professor in the Biochemistry Department.

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Thelen’s soybean plants, which are kept in the fifth floor greenhouse of Bond LSC. | photo by Mary Jane Rogers, Bond LSC

“Each of the [soybean] plants are transgenic and were screened for higher oil content as a result of BADC gene silencing. The plants are harvested every three or four months so the seed oil content can be monitored,” said Ye.

Thelen has begun patenting the BADC technology and another strategy for engineering ACCase to “make it a more efficient enzyme complex.” The BADC technology was co-invented with his previous graduate student, Matthew Salie, who now works as a postdoctoral research associate at the Scripps Research Institute in San Diego. The patent examination process can take years, but if the technology is approved it would mean a huge influx of money in the agricultural market.

“The math is quite simple,” Thelen said. “A one percent increase in soybean seed oil translates to hundreds of millions of dollars. The numbers fluctuate depending on the market, but a one percent increase translates to about 200 million dollars for soybean alone. A five percent increase, which again, I think is achievable, when realized across the diversity of oilseed crops, we’re talking billions in added crop value annually.”

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Yajin Ye, a postdoctoral researcher from China, with Vanildo Silveria and Caludete Santa Cantarina, two visiting faculty from the State University of Rio De Janerio in Brazil. | photo by Mary Jane Rogers, Bond LSC

His innovative approach has gotten the attention of scientists and researchers all around the world. Vanildo Silveria and Claudete Santa Cantarina, two visiting faculty from the State University of Rio De Janerio in Brazil, came to Bond LSC specifically because of Thelen.

“Jay is an expert in the field and we wanted to work with him,” said Silveria.

At the moment, it seems like his research is on the right track. The initial data from Arabidopsis shows that silencing the entire BADC gene family substantially raises seed oil content, which is the main objective of his study.

“Preliminary, first-generation transgenics show soybean with higher oil. But these are greenhouse grown. Randomized field trials are still be awhile out,” Thelen said. “We’re getting closer, but still a few years away from that goal.

Thelen’s most recent oilseed research published in the journal Plant Cell in 2016, titled “A Family of Negative Regulators Targets the Committed Step of De novo Fatty Acid Biosynthesis.” 

Jay J. Thelen is a professor of biochemistry at MU and a researcher at Bond Life Sciences Center. He received degrees in both biological sciences and biochemistry – a B.S. from the University of Nebraska, Lincoln and a Ph.D from the University of Missouri, Columbia. He was a postdoctoral fellow at Michigan State University and has been at MU since 2002.

 

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.

Beverly Agtuca #IAmScience

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Beverly Agtuca was born in New York, but has family in the Philippines, a country that struggles with malnutrition and undernourishment. Her overall goal for her research is to help countries that struggle with undernourishment by increasing the agricultural productivity in those countries.

“When I was little, I went on summer vacation to visit my family, which included my grandmother in the Philippines,” she said. “Everyday my grandmother wanted me to go out to the rice fields from 5 a.m. to 10 p.m. with the other children to get rice for our meals. That was not an easy task and that moment changed my life. That’s when I decided that I wanted to be a plant scientist.”

Agtuca graduated in 2014 with honors in Biotechnology and a minor of Microscopy from the State University of New York College of Environmental Science and Forestry (SUNY ESF) in Syracuse, NY. She’s currently a Ph.D. candidate in plant breeding, genetics, and genomics at MU. She chose to come to Bond LSC because of the community and Dr. Stacey, her supervisor and mentor.

“If you ever need help, there’s always help here,” she said. “Everyone at Bond LSC is so kind, including the staff. I love to make small talk with the custodians and they are always supporting me and say I should never give up when I have a bad day.”

Ever since coming to MU in 2014, Agtuca has been keeping busy. In June, she received a travel award to go to the American Society of Plant Biologists (ASPB) in Hawaii. The International Society for Molecular Plant-Microbe Interactions (IS-MPMI) also awarded her a travel award to attend the 2016 meeting in Portland, Oregon, where she gave an oral and poster presentation. She also has two original research publications under her belt and is currently working in Dr. Gary Stacey’s lab at Bond LSC.

The research for her dissertation is focused on the relationship between rhizobia and soybeans. She collaborates with scientists at George Washington University (GWU) in Washington, D.C. and the Pacific Northwest National Laboratory (PNNL) in Richland, Washington to enhance the capabilities of the 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T FTICR) through application of laser ablation – electrospray ionization mass spectrometry (LAESI-MS) technology that can analyze the contents of single plant cells. This 21T FTICR machine was recently installed at PNNL and represents one of only two such machines in the world.

This is revolutionary because few people do single cell analysis. Usually, scientists deal with the law of averages, which dilutes the final measurements. But this technology gives an in-depth glimpse into a single cell so scientists can obtain a more comprehensive bigger picture.

“After we finish building this technology, we want to spread the technique to different research groups so they can answer these research questions on their own,” said Agtuca. “It can help people outside of plant sciences too, and hopefully will help with cancer treatment and disease prevention.”

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.

 

Samuel McInturf #IAmScience

Samuel McInturf, Ph.D. candidate

Samuel McInturf, Ph.D. candidate

#IAmScience because it’s fun. You’re paid to work with exotic materials and instruments to solve problems that drive at how life manifests.”

Samuel McInturf’s father is an accountant and his mother is an HR director, but somehow he ended up falling in love with science. By the 4th grade he had already asked his parents to buy him a compound microscope. He completed his undergraduate degree in plant biology at University of Nebraska, Lincoln with a minor in biochemistry. Now, he’s finishing up his fifth year pursuing a Ph.D in plant stress biology and works in Dr. David Mendoza-Cózatl’s lab at Bond LSC.

“I mainly came to Bond LSC to work with Dr. Mendoza,” said McInturf. “The work in his lab was right in line with what I wanted to do and I knew the faculty at Bond LSC was great.”

And he’s enjoyed the last five years he’s spent here.

“Bond LSC has vast resources of knowledge and labs are very friendly towards one another,” he said. “So if you are short up on a reagent, or you need to learn to do an assay, someone is always available to lend a hand.”

McInturf’s thesis deals with understanding the genetic factors that balance the uptake and demand for micronutrients – heavy metals – against their toxicity. He specifically looks are regulators of iron and zinc homeostasis.

In addition to his interest in plant biology, he’s also an engineer of sorts. McInturf helps teach a bioengineering class at Bond LSC with undergraduates. The goal of the class is to build robotics that aid laboratory research, and he has taught three of these classes so far.

“I found the change in scale between building widgets in my bedroom to building full scale devices challenging, but ultimately rewarding,” he said.

For undergraduates interested in continuing a career in science, McInturf advises them not to give up, even when things get tough. He admits that he was intent on dropping out of school up until he was 18, but now he’s almost finished with his Ph.D.

“Ten years ago I was very intimidated by what I saw as the difficulty of science and was wavering on whether I wanted to take the dive into a research-heavy field,” he said. “It took a few years to figure that out, so I guess I would have told myself to get a move on and not be so faint hearted about it.”

McInturf isn’t positive where he’s like to be in 10 years, but he’d enjoy continuing to teach and conduct research at a university like MU.

“I’d love to have Dr. Mendoza’s job one day,” he laughed.

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.  

Megan Sheridan #IAmScience

Megan Sheridan

Megan Sheridan, a Ph.D candidate in biochemistry, works in Dr. Michael Robert’s lab. | Photo by Mary Jane Rogers, Bond LSC

By Mary Jane Rogers | Bond LSC

“#IAmScience because it’s extraordinary knowing that a small step towards a treatment could positively impact someone’s life down the road.”

Megan Sheridan doesn’t let anything slow her down.

From presenting at the Society for the Study of Reproduction’s Trainee Research Competition last week—and winning first place—to finishing up her thesis while working in Dr. Michael Roberts’ lab, she’s always juggling multiple projects. Sheridan is finishing up a Ph.D in biochemistry and hopes to graduate in December 2017 or May 2018, depending on how quickly she finishes writing her thesis.

“I was lucky enough to pick up a project studying Zika virus infections early in pregnancy,” she said. “It was one of those perfect timing moments, and we ended up getting some pretty exciting results off the bat. Now I’m really inspired by the direction my thesis work is going and find that my projects are very different but that makes things exciting.“

Sheridan’s thesis focuses on using stem cells as a model for early placenta development and how preeclampsia and viral infections like Zika impact a pregnancy. Preeclampsia is a condition during pregnancy that causes high blood pressure and protein in the urine. The disease likely occurs in the first trimester, but the symptoms don’t evolve until the 2nd or 3rd trimester. To study it, Sheridan uses stem cells generated from umbilical cords of babies born to mothers experiencing preeclampsia or a normal pregnancy, and then uses those cells to determine what defects in the placenta might contribute to the disease preeclampsia.

“I would like to learn as much as possible about the placenta and human pregnancy,” she said. “There are so many unknowns in this area of research because you can’t access the placenta during a pregnancy without disrupting the pregnancy. There are many complications that effect the mother and baby, and if more was known about normal placenta development in pregnancy, then we may be able to better understand and prevent some of those complications.”

Sheridan completed her undergraduate degree at MU, and urges undergraduates to get started in research early, as she believes it gives students a stronger foundation for graduate school. She also believes that mistakes are part of the research process, and wasn’t afraid to share one that she made early on in the Ph. D program.

“I remember in my very first rotation as a graduate student I was learning how to transfect cells with DNA so we could do a reporter assay. We were in the process of adding all the reagents, and between the student I was working with and myself we got confused about who added what,” she laughed. “Somehow, we never added the DNA- an integral part of the transfection! So a week later when we were analyzing the data, we noticed there were no values at all.”

After graduation, Sheridan hopes to experience living outside of Missouri for her postdoc placement. She’d like to stay in academia, and looks forward to continuing to research and teach.

Perhaps one day she’ll even return to MU and Bond LSC!

Kevin Kaifer #IAmScience

Kevin Kaifer

Kevin Kaifer, a Ph.D candidate who works in Dr. Christian Lorson’s lab. | Photo by Mary Jane Rogers, Bond LSC

By Mary Jane Rogers | Bond LSC

“#IAmScience because there are people suffering all over the world and this is where I’m most likely to make any kind of an impact.”

When he came to MU three years ago, Kevin Kaifer knew he wanted to work in Bond LSC. He felt it was where the best science and collaborations were happening on campus, and everything that he needed for his research – a vivarium, a DNA core, and proteomics core – were all conveniently housed here.

“I entered research because I thought the complexity of cellular life is the most fascinating topic in the world,” said Kaifer. “I wanted to be a part of it.”

He completed his undergraduate degree in biology at Truman State University and is currently part of Dr. Christian Lorson’s lab. There, Kaifer is learning transferable skills – everything from communication skills to the production of recombinant gene therapy vectors – all of which will give him a strong foundation for a career in industry.

“The growing promise of gene therapy as a safe and realistic treatment option has led to the start up of many biotech companies that are making really exciting progress,” he said. “This is where I think I will be best able to contribute to science and therapy.”

For undergraduate students who are just getting started in a science field, Kaifer emphasizes that success in science comes and goes.

“In my own personal experience, success in science only comes after a significant set of hurdles,” he said. “You have to be okay with feeling stupid, because part of your job description is to answer questions to which you do not know the answer. I would actually be concerned if you were not struggling to feel successful.”

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.