Natalie Hickerson stands next to her research poster at MU’s Undergraduate Research Forum. Hickerson, a biochemistry major, spent her summer in Dr. Hannink’s lab.
By: Samantha Kummerer| Bond LSC
It takes a lot of time and patience to be a scientist. This is something that first-time researcher Natalie Hickerson quickly discovered.
“A lot of the time things are so small. I mean you’re using such tiny volumes of DNA that you can’t see anything happening,” said the undergraduate biochemistry major.
For some, this uncertainty pair with long lab hours and multiple trial and errors would be frustrating. Hickerson, however, put in the time and asked the questions, which led her to discover the rewards of research.
“You try something a few times and it wouldn’t work and then you change one thing and suddenly it works and you get results and it was just very exciting, like ‘wow what I’m doing is real,’” she said.
Hickerson attends the University of Miami but worked as a research intern in Mark Hannink’s lab in the Bond Life Sciences Center this summer. She said she chose the University of Missouri because the program was well rounded and fit with her major.
Hannink said while Hickerson entered the lab not understanding everything, she wasn’t afraid to ask questions and that helped her catch on fast.
“What makes a scientist different is that you are an active generator of new knowledge. Instead of being a passive consumer of existing knowledge you have to become an active producer of new knowledge,” Hannink said.
The Missouri native spent two months creating new knowledge on PGAM5, an important protein involved in many mitochondrial processes and cell death.
Hickerson began by intensely studying the protein at its most basic level to determine how and why it works the way it does. Part of this process was comparing different mutations of the protein.
Previous research shows how understanding the sensitivity of PGAM5 and its changes in the cell could help in nerve-degenerate diseases like Parkinson’s and ALS. Individuals suffering from those diseases experience a loss of function or mutation in some proteins.
Part of Hickerson’s initial research aimed at figuring out what signal activates PGAM5 in a cell. A better knowledge of that process will help scientists understand how pathways function and turn off during nerve-degenerative disease.
Hannink explained if a pathway is defective, activating a different pathway may function as a type of therapy.
After months of long hours, Hickerson discovered by changing the pH levels, PGAM5 can be switched from inactive to active.
“We had suspected it to be the case but the data she provided really helped demonstrate that was true,” Hannink said.
While Hickerson is headed back to Florida to continue her pursuit of biochemistry, her findings will continue to be advanced this fall in Hannink’s lab.
“There’s a lot more to be discovered with what we were doing,” Hickerson said. “A lot of the stuff we were doing this summer was new ideas and just developing deeper knowledge on things they’ve discovered in the lab previously. So, I was looking deeper into what they already started and we did find some new things so it was neat.”
She said her experience this summer inspired her to get more involved in undergraduate research.
“It definitely gave me a much better understanding of how to work in a lab and just basic lab techniques. The overall research project gave me a lot of good foundation for that,” she said.
As Hickerson continues to learn about research, Hannink said it’s an ongoing process that he is still a part of.
“I’m doing the same thing all the time that they are learning to do,” he said. “There’s this dynamic and that active learning process also challenges me to becomes a better scientist as well.”
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.
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.”
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.
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
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.
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.”
Yajin Ye, a postdoctoral researcher from China, adds water to the plants. | 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.
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.”
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.
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.”
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.
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.
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.
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.
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.
Katelynn Koskie, a Ph.D. candidate, waters young Arabidopsis plants. Koskie studies what causes changes to a plant mutation called HPH. | Photo by Samantha Kummerer, Bond LSC
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.
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.
Ph.D. student Johanna Morrow holds up a dish of three-day-old genetically modified 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.
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.
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.
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.
Johanna Morrow collects her samples of leaf tissues from liquid 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.
Katelyn 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 LSCA 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.
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.
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.
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.
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.
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.
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.
“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.
How bossy insects make submissive plants create curious growths
By Samantha Kummerer | Bond LSC
They are bumps on leaves, bulges in stems and almost flower-like growths from plant tissue with a striking amount of variety. They are galls.
These unnatural growths garnered the curiosity of Jack Schulz for years. While he’s spent 40 years studying topics from Insect elicitors to habitat specialization by plants in Amazonian forests, what he’s really wanted to study was galls.
“It’s so weird,” said Schultz, director of the Bond Life Sciences Center. “I’ve always been really curious about how these strange structures form on plants.”
Schultz has spent the last two years trying to answer that question, looking at their development and the underlying genetic changes that make galls possible.
He’s not alone in his fascination.
“I found my very first gall when I was a masters student,” said Melanie Body, a postdoctoral researcher in Schultz’s lab. “I was really excited because it was here the whole time, I just didn’t see it. One of my teachers showed me and it was like a revelation, basically, what I wanted to work on.”
These “strange structures” are often mistaken for fruit or flower buds on a variety of plants from oak trees to grapevines and there’s a good reason why…
“A gall on a plant is actually, at least partly, a flower or a fruit in the wrong place,” Schultz said.
Galls on a leaf. The leaf’s red bumps are not natural, but caused by tiny insects. Inside each gall is many tiny insects. | photo by Melanie Body
These galls can be the size of a baseball or the size of a small bump depending on the plant. They can also range from just small green bumps on the undersides of leaves to vivid complex growths of color.
Despite the variety, the one thing consist across plants is that the gall is not there by the plant’s choice.
“The insect has a pretty good strategy because it starts feeding on the plant and it will create a kind of huge structure, huge organ, where it can live in, so it’s making it’s own house,” Body said.
The reasoning behind the formation is relatively unknown, however, it is hypothesized that the insect flips a switch within the plant. The insect is not injecting anything new, but rather turning off and on certain genes within the plant.
Schultz explained the galling insect has the power to changes the expression of genes and in some instance disorient the plant’s determination of what is up from down.
The Problem
So how does this affect the plant?
Not only is the insect creating the gall against the plant’s nature, it is also using the plant’s energy and materials for the job.
“I think it’s very cool to imagine an insect can hijack the plant pathway to use it for its own advantage,” Body said.
The view of a gall from under a microscope. The mother insect is the orange figure in the foreground and is surrounded by her eggs. | Photo by Melanie Body
The insect receives protection and a unique food source and in turn, the plant is left with fewer resources.
“From the plant’s point of view that’s all materials that could have gone into growth and reproduction, so you can think of these galling insects as competing with the plant they’re on for the goodies the plant needs to grow and reproduce,” Schultz explained. “That’s not so good for producing grapes.”
Grapevines are just one of the many plants that galls can form on, but also the plant Schultz’s research uses.
“In our case we work on grapes, so it can be a big issue if the fruits are not sweet enough anymore, because if you don’t have sugar in the fruit then it’s not good enough for the wine production, so it’s pretty important,” Body explained.
Researcher Melanie Body searches the grapevines for galls at Les Bourgeois Vineyards. | Photo by Samantha Kummerer, Bond LSC
In Missouri, the story of grapevines and galls goes back to the 1800’s.
The story goes, the phylloxera insect found its way over to France. Soon it spread throughout the country; wiping out vineyard after vineyard.
“The great wine blight and the world was going to lose all wine production because of this pest,” said Schultz.
Luckily, a small discovery in native Missouri grapevines led to a solution that allowed wine drinkers to rejoice and scientists to puzzle.
“There’s something about the genes in Missouri grapevines that protects them against this insect,” Schultz explained.
While the European wine industry faced extinction, the phylloxera insect, coexisted with native Missouri grapevines. So, now every grapevine in a vineyard is grafted with insect-resistant roots from Missouri grapes.
But, no one really understands what’s so special about grapevine roots in Missouri.
The research
These galls aren’t new. They’ve actually existed for up to 120 million years. But, here’s what is:
“When we started this research, we thought this is a really well-studied insect,” Schultz said. “It turns out there is an awful lot we don’t know about them.”
The team collects samples of galls from grapevines at Les Bourgeois. Back in the lab the galls are dissected using very small tools and then examined with a microscope. Under the microscope, a colony of the insects emerges. The otherwise miniscule mother insect and her 200 eggs can be seen alongside other insects just moving around the gall.
Researcher Melanie Body examines a grapevine gall under a microscope. Body is a member of Jack Schultz’s lab that studies galls and the insects that create them. | Photo by Samantha Kummerer, Bond LSC
Body compares the insects’ round textured bodies to oranges but with two black eyes.
Schultz’s team hypothesized that there are specific flower or fruit forming genes that are necessary for the insect to create a gall.
To answer this, the team looks at which genes are turned on when the insect creates the formation of a gall. Those observations by themselves don’t prove which genes are essential. So, next, the researchers manipulate the genes by changing the gene’s expression.
“If we find that Gene A is always on when the insect causes a gall to form, we can stop the expression of Gene A to test the hypothesis that it needs gene A to get the gall to form,” Schultz explained. “We can ask a plant. If you lack Gene A, can our insects still form galls?”
The researchers are still analyzing the results, but the current findings suggest that some genes do reduce the insect’s ability to make a gall.
A microscopic view of a galling insect in the process of creating a gall. The gall is forming around the insect. | Photo by Melanie Body and David Stalla
Since beginning the research two years ago, Schultz said he has discovered, “all kinds of crazy things”.
Schultz said it was previously believed that the insect was staying in one place when making the circular gall, but actually, the little insect is moving around; something no one realized before.
And that’s not the only myth this research is debunking. For example, many believe there is one insect per gall, but this turns out to be incorrect. The gall can actually become a hospital of sorts where many mother insects flock to move in and lay their eggs.
And although galls sounds like an odd area of study, the research actually falls under basic developmental biology.
Schultz said research on galls could lead to discoveries about flowering and fruiting.
“Finding a situation in which flower or fruit structures are forming in odd places is actually suggesting to us, pathways and signals that are probably not as well studied in developmental – normal flowers and fruits,” Schultz said.
Beyond curiosity, one of the reasons to study the galls is to find a way to reduce the number of pesticides used on grapevines. The small size of the galling-insect causes grape growers to spray a lot of chemicals.
There’s a lot of discoveries, a lot of implications, but also still a lot of unknowns. Schultz doesn’t let that discourage him.
“If we knew everything about all kinds of things in nature, I’d be out of business and we’d have nothing to do,” Schultz reassured.
The curiosity behind the research continues to hold true for both Schultz and Body outside the lab. From collecting galls for each other to photographing the mysterious spheres, the two are always on the look out for the hidden work of the tiny insect.
Research quadruples speed and efficiency to develop embryos
New research makes IVF four times more efficient to create pigs like this for genetics research and breeding in labs like that of Randy Prather at MU. | Photo by Nicholas Benner.
By Samantha Kummerer | Bond LSC
What started as a serendipitous discovery is now opening the door for decreasing the costs and risks involved with in vitro fertilization (IVF).
And it all started with cultured pig cells.
Dr. Michael Roberts’ and Dr. Randall Prather’s laboratories in the University of Missouri work with pigs to research stem cells. During an attempt to improve how they grew these cells, researchers stumbled across a method to improve the success of IVF in pigs.
“Sometimes you start an experiment and come up with up with a side project and it turns out to be really good,” Researcher Ye Yuan said.
The Prather lab in the MU Animal Sciences Research Center uses genetically modified pig embryos to improve pig production for agriculture and also to mimic human disease states, such as cystic fibrosis. Roberts’ team in the Bond Life Sciences Center occasionally collaborates with Prather’s lab to produce genetically modified pigs for this valuable research. However, the efficiency of producing these pigs is very low because it depends on multiple steps.
First, scientists remove oocytes (“eggs”) and the “nurse” cells that surround them from immature female pig ovaries and place the eggs in a chemical environment designed to mature the eggs, allowing them to be fertilized in vitro with sperm from a boar. This process creates zygotes, which are single-celled embryos, that are allowed to develop further until they become hollow balls of cells called blastocysts about six-days later. These tiny embryos are then transferred back into a female pig with the hopes of achieving a successful pregnancy and healthy piglets.
However, Roberts said the chance of generating a successful piglet after all those steps is very low; only 1-2 percent of the original eggs make it that far.
The quality of the premature eggs and the process of maturing them significantly reduces the rate of success.
“In other words, all this depends on having oocytes that are competent, that is they can be fertilized, form blastocysts and initiate a successful pregnancy,” Roberts explained.
Normally, researchers overcome the low success rate by starting out with a very large number of eggs, but this takes lots of time and money.
So, lab researchers, Ye Yuan and Lee Spate, began tinkering with the way the eggs were cultured before they were fertilized, making use of special growth factors they used when culturing pig embryonic stem cells.
Yuan and Spate added two factors called fibroblast growth factor 2 (FGF2) and leukemia inhibitory factor (LIF).
This combination helped more than the use of just a single factor and so they decided to add a third factor, insulin-like growth factor 1 (IGF1).
Together the three compounds create the chemical medium termed “FLI”.
“It improved every aspect of the whole process,” Roberts said. “It almost doubled the efficiency of oocyte maturation in terms of going through meiosis. It appeared to improve fertilization and it improved the production of blastocysts.”
In all, the use of FLI medium doubles the number of piglets born and quadruples the efficiency of the entire process from egg to piglet.
While the researchers are still figuring out why the three factors work together so well, Roberts believes it has to do with the fluid that surrounds the immature eggs while they are still in the ovary.
Roberts explained that unusual metabolic changes happen in the eggs and their nurse cells when the three components are used in combination but not when they are used on their own. These components are also found in the follicular fluid surrounding the egg when it is in the ovary.
However, follicular fluid actually contains factors that hinder egg maturation until the time is right, so it would seem counterintuitive to add the fluid to a chemical environment aimed at maturing the eggs. However, when freed from the other components of follicular fluid, the three growth factors act efficiently to promote maturation.
“It just creates this whole nurse environment for that egg. Once you’ve done that you’ve sort of patterned them to do everything else after that properly — fertilization, development of that fertilized egg to form a blastocyst, and the capability of those blastocysts to give rise to a piglet,” Roberts said.
Researchers hope the FLI medium can be translated beyond genetically modified pigs.
“If we could translate this to other species it could be more meaningful,” Yuan explained.
For the cattle industry, FLI has the potential to decrease the time between generations in highly prized animals.
Currently, if an immature dairy cow has desirable traits, the industry has to wait a year or so for that cow to mature and for its eggs to be collected. Using FLI medium immature eggs could be retrieved when the prized female is still a calf. After fertilizing them with semen from a prized bull, production of more cows with desirable traits could be achieved in a shorter amount of time.
The potential implications of this discovery aren’t just for farm animals.
Yuan said if this treatment could be applied to humans it would be a big help for both the patient and the whole field of human IVF.
Currently, in vitro fertilization for humans comes with high costs and risks.
“You try to generate a lot of eggs from the patients by using super-high doses of expensive hormones, which is not necessarily good for the patient and can, in fact, be risky. ” Roberts explained.
These eggs are then collected, fertilized, and the best-looking embryo transferred back to the patient. As in pigs, this overall process isn’t all that efficient. The hope is that the treatment of the patient with hormones can be minimized if immature eggs are collected directly from the ovary by using an endoscope and matured in FLI medium, allowing them to be just as competent as those retrieved after high hormone treatment.
“The idea is it would be safer for the woman, it would be cheaper, and it might even achieve a better success rate,” Roberts said.
The team still has some time before knowing for sure if FLI medium is applicable in other mammals.
Yuan said the focus is now on understanding the mechanism behind how the three compounds work so well together.
For now, preliminary data are being collected with mice and a patent is awaiting approval. Still, the team has high hopes for this almost accidental finding.
“Whenever you’re doing science, you’d like to think you’re doing something that could be useful,” Roberts said. “I mean when we started this out it wasn’t to improve fertility IVF in women, it was to just get better oocytes in pigs. Now it’s possible that FLI medium could become important in bovine embryo work and possibly even help with human IVF.”
Michael Roberts is a Bond LSC scientist and a Curators’ Distinguished Professor of Animal Science, Biochemistry and Veterinary Pathobiology in the College of Agriculture, Food and Natural Resources (CAFNR) and the College of Veterinary Medicine. He is also a member of the National Academy of Sciences.
Randall Prather is a Curators’ Distinguished Professor of Animal Science in the College of Agriculture, Food and Natural Resources (CAFNR) and Director of the National Institutes of Health funded National Swine Resource and Research Center.
How an MU student helped start a Twitter trend and how social media is advancing science.
By Mary Jane Rogers | Bond LSC
In the modern age, science isn’t a solitary endeavor.
You might be a tweet away from connecting with scientists about their work, as one MU student recently proved.
Dalton Ludwick, an MU doctoral student in entomology, helped spur a hashtag trend to connect real scientists with none other than Bill Nye.
If you follow any scientists on Twitter, you may have come across the hashtag #BillMeetScienceTwitter while scrolling through your feed. Thousands of scientists on Twitter introduced themselves to the famous TV host of Bill Nye the Science Guy using the hashtag. By May 22, a mere three days after the hashtag started, more than 27,000 scientists and experts had tweeted at Nye.
#BillMeetScienceTwitter was born from a Twitter discussion between Ludwick, London-based zoologist Dani Rabaiotti and New Zealand-based marine biologist Melissa Marquez.
“Bill Nye Saves the World” is a television show currently streaming on Netflix hosted by Bill Nye. The first season explores topics such as climate change, alternative medicine and video games.
The original sentiment behind the hashtag was something scientists have long been discussing — that Nye’s television show doesn’t include a diverse array of science experts to answer questions outside Nye’s specialty. On Season One of his show, a majority of the experts Nye invited were comedians, supermodels and Hollywood stars, like Karlie Kloss and Zach Braff.
We were curious about the origins of this campaign, so we reached out to Ludwick, one of the creators of the hashtag.
Ludwick regularly uses social media to reach out and connect with other scientists. He meets other scientists on Twitter, shares ideas and often turns that conversation into a real-life, professional relationship on a global scale.
Dalton Ludwick, a Ph.D candidate in Entomology at MU and one of the creators of #BillMeetScienceTwitter.
“I talk to people from the UK, Australia and New Zealand on social media,” he said. “It’s a great way to connect with people.”
Social media is a game changer for scientists who once felt walled off from the broader world. It can be a great way to connect with people doing similar research, track grants and jobs, share exciting breakthroughs, and follow conferences.
Jared Decker, an assistant professor in the College of Agriculture, Food and Natural Resources at MU, is another avid social media user on campus. He uses Facebook, Twitter and YouTube accounts to connect with other science professionals and academics, as well as his public — mainly beef and cattle producers and farmers.
Jared Decker, an assistant professor in the College of Agriculture, Food and Natural Resources at MU.
“Just the other night I was writing a grant and one of the reviewers had a specific criticism,” he said. “So, I got on Twitter and asked my question. A colleague of mine was online in Australia and was able to respond to make sure we were meeting the guidelines.”
Scientists used to have to walk down the hall to ask a colleague, or play phone tag with someone abroad.
“You can’t do that at 1 a.m.,” said Decker, “but you can go on Twitter.”
Many scientists believed that Nye’s television show wasn’t utilizing his vast array of science connections to find experts in specific fields of science.
“If you ask me about biology or oncology, I probably shouldn’t answer because that’s not my area of expertise,” said Ludwick.
In response to a tweet by Rabaiotti, Mike Stevenson was the first to ask if anyone had reached out to Nye on Twitter. Ludwick replied to that conversation with the hashtag #BillMeetScienceTwitter, which was meant to show Nye the diversity of scientists on social media.
Rabaiotti – a Ph.D candidate at University College London, who studies the effects of climate change on wild dogs in Africa – was the first to introduce herself to Nye.
Overall, the tweets and engagement have been overwhelmingly positive.
We decided to tweet at Nye too!
“What we were actually trying to do was reach out and offer assistance in areas outside the expertise of Bill and Neil,” said Ludwick. “We wanted to show the diversity of people doing science, as well as the diversity of the science that we do. More than 50 percent of the people tweeting on #BillMeetScienceTwitter were women — certainly not just a bunch of nerdy men in lab coats!”
Ludwick adds that the hashtag wasn’t intended as an attack on Bill Nye or Neil deGrasse Tyson, another scientist celebrity with broad reach. Instead, the point was to let them know that fellow scientists exist and can be a great source for accurate scientific information.
Nye responded to the hashtag, and even took the time to retweet and reply to his favorite posts.
Overall, the hashtag was a huge success, brought awareness and engaged scientific topics. But more than that, it shows how responsive and positive the scientific community can be. Some news articles noted that the campaign was “trolling in the politest way possible.”
“The scientific community on Twitter is really welcoming,” Decker said. “It doesn’t matter if you’re a first year science student or an endowed professor. People don’t treat you any differently.”
And an online presence is vital for scientists and their careers. In 2007, BioInformatics LLC conducted a survey of 1,510 scientists with regard to how they used social media. They found:
77% of life scientists participated in some type of social media
50% viewed blogs, discussion groups, online communities, and social networking as beneficial to sharing ideas with colleagues
85% saw social media affecting their decision-making
For junior scientists or researchers who are just getting started, Decker has some advice.
“Tweeting out at conferences is a good way to practice taking in an idea and getting it back out there in written form,” Decker said. “Instead of taking notes, tweet out what you would have written down.”
#BillMeetScienceTwitter also helped bridge the gap between scientists and the public. Ludwick said that this hashtag helped flip the public perception that scientists are only old men in lab coats on its head.
“People were saying, ‘Hey, I’m going to show my daughter this and inspire her,’” Ludwick said.
Ludwick also thinks that, in general, social media makes him better at communicating science to the public.
“Twitter is a great way to break things down and stop using scientific jargon,” he said. “I think it has helped me personally and it’s great practice.”
Decker agrees with Ludwick’s assessment.
“The first few months on the job it felt like I was back in Spanish class,” he joked. “I was taking the science jargon and doing mental gymnastics to translate it into the language a lay person would understand. But, now I’m fluent in both!”
So, think twice the next time you consider social media to be a waste of time. Whether it’s a hashtag that brings issues to the attention of science celebrities, platforms that connect scientists at a global level or posts that make research more accessible, social media has done a pretty cool job of advancing science.
Graduate Researcher Sarah Unruh explores the essential role of fungi in orchid germination
Graduate Researcher Sarah Unruh | photo by Emily Kummerfeld, Bond LSC
By Emily Kummerfeld | Bond LSC
The blooms of orchids are unmistakably beautiful, and how they reproduce has fascinated biologists for centuries.
But, orchids might not even exist if not for the help of fungus. Up to 30,000 species of orchids require the intervention of fungi since their seeds do not contain the necessary nutrients to sprout.
Sarah Unruh, a fifth-year biological sciences PhD student in the lab of Bond LSC’s Chris Pires, seeks to discover and record the specific types of fungi utilized by many orchid species. By studying their specific genetic expressions, she hopes to uncover what allows these fungi to interact with orchids in this way, how these fungi are related to each other and what genes each organism is expressing with and without each other.
A blooming orchid in the Tucker greenhouse. Although this orchid grows in a pot, like most species of orchid it is an epiphyte and naturally grows on tree branches. | photo by Emily Kummerfeld, Bond LSC
“The main question for me is, what is the nature of this relationship? Is it more mutualistic or parasitic? You don’t often get something for nothing, so why is the fungus participating in this relationship? Most fungi that live in plant roots receive carbon from the plant. Orchid fungi are doing the opposite and that is weird. I want to know how this relationship works,” Unruh says.
Unruh first studied orchid evolution and how each orchid species related to each other genetically. “My assumptions of what a plant was were so violated by orchids and it still fascinates me! So many orchid species grow on trees, many don’t have leaves, some species never even turn green or photosynthesize.”
This focus soon evolved into her interest in the relationship between orchid plants and fungi. Fungi are neither plants nor animals, and have their own branch on the eukaryotic family tree. They are nonetheless essential to plant biology, “eighty percent of plant species have beneficial fungi in their roots,” says Unruh.
Many orchids are technically classified as epiphytes, which means they grow on the surface of another plant and get all their food and water needs from the air, rain and what accumulates nearby. That doesn’t leave a lot of extra nutrients to put into seeds, which typically need the store of food to sprout and grow its first leaves.
Germinating orchids seeds. A small mass of fungus is placed in the Petri dish to assist in germination. | photo by Emily Kummerfeld, Bond LSC
That’s where fungi come into play. Some types of fungi can even germinate several species of orchids, and studying the DNA sequences of these fungi could be vital in the future for endemic endangered orchids and their associated fungi. “I’ve always been interested in relationships between organisms or symbioses,” says Unruh, “the fact that orchid seeds need fungi to survive was too weird not to research.”
Tulasnella calospora, nicknamed the “Super Fungus”. This type of fungus can germinate several species of orchids. | photo by Roger Meissen, Bond LSC
But the process of studying fungi DNA is not a simple one.
“In order to look at their genomes, I need to grow a lot of fungi and then grind it up and add certain substances to isolate only the DNA. I send this DNA to a facility called the Joint Genome Institute where they send it through a machine that spits out a file with a list of lots of small pieces of the genome – like puzzle pieces. I then use computer programs to put the pieces together and try to assign a function to each gene.”
So, the established relationship between fungus and seed helps the orchid, but it’s not known what the fungus is getting out of this arrangement. One idea, based on recent published research, is the fungi receives a certain form of nitrogen from the orchid seeds. Another experiment Unruh is working on is growing the orchid seeds by themselves through special media, growing the fungus by itself, or growing them together. She then measures the gene expression to see if there are big differences when the plant or fungus is alone or together. “This will help answer my question of how mutually beneficial this association is,” says Unruh.
The data collected from this research will form the bulk of her PhD thesis. However, there remains many questions regarding the relationship between orchids and fungus that Unruh would like to explore in the future, such as which fungi are best for reintroducing endangered orchid species or what other roles fungi play in their environment. “I foresee fungi, especially plant and fungal relationships, becoming the focus of more and more research in the future.”
In 2014, Unruh received a three-year National Science Foundation (NSF) Graduate Research Fellowship. More recently, she has received a grant from the Joint Genome Institute to sequence 15 full genomes of orchid fungi.
