soybeans

#IAmScience Jordan Brungardt

March 26, 2021 By Becca Wolf in #IAmScience Tags: Legume, soybeans

By Becca Wolf | Bond LSC

When one hears of a magician, they think of a man that pulls a rabbit out of a top hat or ‘cuts’ people in half. Magicians have a lot of tricks up their sleeve.

People do not think of scientists as magicians, yet they still perform wonderous things.

“I heard a quote one time that says science and technology is kind of like magic,” Jordan Brungardt said. “For somebody that doesn’t know what is happening, experiments look like magic if they’re performed well. Think of cell phones allowing us to talk to people across the world. For somebody from a few decades ago, that would seem like magic.”

For Brungardt, a post-doctoral fellow in the Gary Stacey lab at Bond Life Sciences Center, this magic of sorts makes research exciting.

“When you get sequencing information back in the lab after going weeks without actually seeing something and it lines up with what you’re predicting, it’s like Christmas,” Brungardt said.

In the Stacey lab, Brungardt studies the genes involved in early nodule development in soybeans.

He looks at the interaction between rhizobia, a species of bacteria, and their plant hosts, legumes. His work aims to explore how the plants allow access to their inner roots through infection thread development.

“They undergo an intimate interaction that is really unique,” Brungardt said. “It’s pretty cool from that aspect, and the infection thread is an important part of the interaction.”

Brungardt currently works with Jaehyo Song, a postdoctoral student in the Stacey lab.

“He is a very careful person, and experimenting together helps prevent any mistakes,” Song said. “I can also see that the experiment is progressing step by step because we work very diligently.”

The two have been working together for a few months and have found their collaboration to be very beneficial.

“Even when a simple problem occurred in the experiment, he did not ignore it,” Song said. “He found the exact cause of the problem through previous research and eventually solved it. Through this, I could see that his problem-solving skills were very good.”

Brungardt is able to dodge problems that arise in his research easily.

“There’s a lot of different facets of my research,” Brungardt said. “If I get stuck somewhere, I can make headway somewhere else, which allows me to take my time on the process that I’m stuck on and come back to it later.”

Brungardt completed his undergraduate degree at Fort Hays State University in Kansas and his master’s degree at Wichita State University. That wasn’t his initial plan, though.

“I knew I wanted to do something with soybeans coming out of my undergrad and, to be honest, I actually interviewed with Dr. Stacy, who is my mentor right now, but it didn’t work out,” Brungardt said. “So, it was really nice coming back and getting a job here, because that’s what I initially wanted to do.”

Even though Brungardt did not initially come to Mizzou, he remained focused on it as the end goal. He ended up getting a job as a microbiologist where he produced Rhizobia for farmers to use to improve their crop production.

“My Ph.D. dealt with microbial interaction with plants, so it still had some loose application for what I’m doing now,” Brungardt said. “While my path wasn’t straight, it never strayed from what I wanted to do. I liked that I still did things that were relevant to what I wanted to do.

Brungardt arrived at Bond LSC last June and has adjusted nicely. His research is similar to what he has done previously, just in a new building in a new lab. He is happy to finally be able to completely focus on his research.

“I just graduated with my Ph.D. last year so there’s no more homework or classes for me. It’s a little bit of a change,” Brungardt said. “It’s simpler, I don’t have to break up my workday to go to class and then come back and work, and then switch up to something again. As a student I was doing several things at once and had other things in the back of my mind. Now I can just focus on my research.”

Since Brungardt can devote all of his time to his research now, he expects to see a lot more magical moments in the lab.

#IAmScience Bruna Luz

May 1, 2020 By Lauren Hines in #IAmScience Tags: soybeans

By Lauren Hines | Bond LSC

At four years old, first year Ph.D. student Bruna Luz was running around and catching bugs in her backyard just to stare at them, trying to understand how they worked.

“Biology has always been part of my life,” Luz said.

Now, Luz studies soybean genetics and how soybeans interact with rhizobia in the Gary Stacey lab at Bond LSC.

Rhizobia are bacteria that fix nitrogen in the soil, providing nutrients to the soybean plant. In exchange, the bacteria feed off of photosynthesis products created by the plant, forming a symbiotic relationship. Luz and the Stacey lab are trying to further understand the genetic factors of this relationship.

If researchers can understand and therefore manipulate this interaction, this nitrogen-providing ability can be transferred this nitrogen-providing ability to other plants that require large amounts of nitrogen, such as corn. This way, farmers cut costs by not having to add nitrogen fertilizers, and it would decrease the environmental effects like water pollution from fertilizer runoff and greenhouse gases created from excess gas emissions from soil microbe metabolism.

“I am a biologist and from my perspective, it’s interesting to see how this area can affect the environment because the increase of agriculture has been crazy, and we’re not doing much to avoid environmental impact,” Luz said.

By solely relying on the natural production of nitrogen for plants, farmers could decrease the amount of nitrogen fertilizer used in their agriculture activities. Even though helping the environment is a large motivation for Luz, the study hasn’t reached the applied research phase.

“What we are doing is basically trying to discover new things,” Luz said. “So, my biggest motivation is knowledge and trying to understand how things actually work.”

Luz decided to pursue her Ph.D. at Mizzou after talking with Gary Stacey, professor of plant sciences and biochemistry, when he visited the Federal University of Paraná in Brazil (UFPR). Luz graduated from UFPR in the spring of 2019 and enrolled at Mizzou in the fall.

Other than going to Canada in high school, Luz hasn’t traveled much outside of Brazil.

“I think [the transition] was pretty smooth,” Luz said. “The first few days were kind of shocking, just from seeing people dress a little differently and sometimes not understanding what people say. I used to be an English teacher back in Brazil…I understand mostly everybody, but there were some people that took me a while in the beginning.”

Luz’s husband and dog joined her in Columbia in October.

“It was more of a transition as a family here,” Luz said. “It’s been a little harder for my husband who is new to the country and has never been to an English-speaking country before.”

However, she says the dog is fine.

Whether Luz is in the lab or working from home, her curious nature drives her, just like when she was four years old.

#IAmScience Bing Stacey

April 17, 2020 By Lauren Hines in #IAmScience Tags: soybeans

By Lauren Hines | Bond LSC

Bing Stacey works on her soybean genetics papers in her office with the company of a plant on the windowsill and a large tropical photo of the Philippines on the second floor of Bond LSC. For the past few years, Bing Stacey has been working towards uncovering the secrets of soybean genes.

That work aims to identify what different genes do within the soybean genome so that they can be manipulated and create higher crop yields. Soybeans are a major source of cooking oil and protein in animal feeds.

Even though Bing Stacey has been at Bond LSC for over a decade as part of the lab of her husband, Gary Stacey, she got her own lab about six years ago when she received her own funding.

Walter Gassmann, interim director for Bond LSC, collaborated with Bing on a project when she was still part of the Gary Stacey lab.

“I said she worked in Gary’s lab, but she was very much the driver of that project,” Gassmann said. “It’s not like she needed to be told what to do. She’s a very experienced biologist.”

Bing Stacey started her research career abroad as a research assistant at the International Rice Research Institute in the Philippines. In 1989, she went to school in Vermont and quickly transferred after finding how cold Vermont was. By the way, she says Missouri is slightly better.

After getting her Ph.D. in microbiology from the University of Tennessee, she found her interest in plants during her post doctorate. Finally, in 2002, Bing found herself at Bond LSC.

“I see my research as facilitating gene discovery to improve agronomic traits of soybeans,” Bing Stacey said.

Currently Bing Stacey’s work identifies which genes are responsible for which phenotypes or physical traits in soybean plants.

“The genome of the soybean is pretty complex and redundant,” Bing Stacey said. “So, it’s kind of hard to discover genes that are important for improving agronomic traits of soybean.”

More specifically, she is studying possible genes that could control plant size and the number of seeds in each pod.

So far, she has found the gene controls for vitamin E content and the gene that matches a quantitative trait locus (QTL) found in another study.

“There is a major QTL that has been published,” Bing Stacey said. “The Chinese actually have been mapping them. I think we have the gene for that QTL…So, my research has the potential to get to the genes that are influencing important agronomic traits.”

Bing Stacey uses fast neutron and CRISPR CAS9 methods to target certain genes and prove they are responsible for causing a certain physical trait. Fast neutron and CRISPR are helpful because they’re able to locate, target and edit specific genes to establish relationships between traits and their genes.

She says she’s “really quite excited” and “strongly believes” in these methods for achieving her goals.

After having the chance to go her own way, Bing Stacey has found success in her work.

“I was very glad for her to get that non tenure track position a few years ago,” Gassmann said. “She’s always been independent minded, and now she has more independence.”

Even though Bing Stacey has already made great strides in finding the links between phenotypes and genes in the soybean genome, there is still a lot left to uncover.

“I think it’s the discovery,” Bing Stacey said. “[I really like] the discovery of new knowledge that comes with science.”

#IAmScience Eric Fedosejevs

February 16, 2018 By Allison Scott in #IAmScience Tags: soybeans

By Allison Scott | Bond LSC

“#IAmScience because I want to discover how plants decide what to store in their seeds.”

The family garden doesn’t typically turn into a life-long journey of studying plants. But when Eric Fedosejevs went to college, the native Canadian found that plants naturally made sense when deciding what to do with his life.

“Growing up, we always had a big garden with a lot of vegetables,” Fedosejevs said. “And with the ever-present need to increase food supply and address world hunger, combined with the innovation in plant-based technologies, there seemed like a lot of potential in plant biology.”

As a postdoc in Jay Thelen’s lab in Bond LSC, Fedosejevs has gone from longtime student to full-time researcher.

“A major focus of the Thelen lab is to look at oil biosynthesis in developing seeds,” Fedosejevs said.

Specifically, Fedosejevs works with soybean, which is a key crop in the United States because it has such a high protein content. But oil production suffers because of the high protein and his focus is looking at altering that part of the seed.

“The oil content of soybean is not as high as most oil seeds,” Fedosejevs said. “The goal of my project is to boost that content without causing any significant decrease to the valuable protein.”

In his role as a postdoc, Fedosejevs has the freedom to do what he loves with the guidance of an established researcher in Thelen.

“This experience has been great,” Fedosejevs said. “Jay gives a lot of research freedom to his postdocs, so I’ve been able to bring many of my own ideas into my project. I appreciate that a lot.”

When he’s not in the lab working on soybeans, Fedosejevs can be found reading about anything that piques his interest.

“I can spend a whole day reading about a topic I know nothing about,” Fedosejevs said.

It is that dedication to learning that landed him in academia, and it’s also what guided him to a career as a researcher. Fedosejevs, however, believes that genuine curiosity is the foundation for being successful in science.

“If you have that mindset and you find a research area you’re also passionate about, a postdoc is very much something to look forward to,” Fedosejevs said.

He’s able to focus all of his energy on his work, and he loves it.

“I’m really happy coming to work and doing research every day.” Fedosejevs said. “I’m going to keep doing that for as long as I can.”

Drowning in Data

August 18, 2017 By Roger Meissen in Research Tags: big data, bioinformatics, KBCommons, Soy KB, soybeans

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.

Chemical persuasion

February 10, 2017 By Roger Meissen in Research Tags: mimics, nematodes, peptides, soybeans

Scientists prove parasite mimics key plant peptide to feed off roots
By Roger Meissen | Bond LSC

A nematode (the oblong object on the upper left) activates the vascular stem cell pathway in the developing nematode feeding site (syncytium) on a plant root. | contributed by Melissa Mitchum — A nematode (the oblong object on the left) activates the vascular stem cell pathway in the developing nematode feeding site (syncytium) on a plant root. | photo by Xiaoli Guo, MU post-doctoral research associate

When it comes to nematodes, unraveling the root of the issue is complicated.

These tiny parasites siphon off the nutrients from the roots of important crops like soybeans, and scientists keep uncovering more about how they accomplish this task.

Research from the lab of Bond LSC’s Melissa Mitchum recently pinpointed a new way nematodes take over root cells.

Melissa Mitchum | photo by Roger Meissen, Bond LSC

“In a normal plant, the plant sends different chemical signals to form different types of structures for a plant. One of those structures is the xylem for nutrient flow,” said Mitchum, an associate professor in the Division of Plant Sciences at MU. “Plant researchers discovered a peptide signal for vascular stem cells several years ago, but this is the first time anyone has proven that a nematode is also secreting chemical mimics to keep these stem cells from changing into the plant structures they normally would.”

Stem cells? Xylem? Chemical mimics?

Let’s unpack what’s going on.

First, all plants contain stem cells. These are cells with unbridled potential and are at the growth centers in a plant. Think the tips of shoots and roots. With the right urging, plant stem cells can turn into many different types of cells.

That influence often comes in the form of chemicals. These chemicals are typically made inside the plant and when stem cells are exposed to them at the right time, they turn certain genes either on or off that in turn start a transformation of these cells into more specialized organs.

Want a leaf? Expose a stem cell to a particular combination of chemicals. Need a root? Flood it with a different concoction of peptides. The xylem — the dead cells that pipe water and nutrients up and down the plant — requires a particular type of peptide that connects with just the right receptor to start the process.

But for a nematode, the plan is to hijack the plant’s plan and make plant cells feed it. This microscopic worm attaches itself to a root and uses a needle-like mouthpiece to inject spit into a single root cell. That spit contains chemical signals of its own engineered to look like plant signals. In this case, these chemicals — B-type CLE peptides — and their purpose are just being discovered by Mitchum’s lab.

“Now a nematode doesn’t want to turn its feeding site into xylem because these are dead cells it can’t use, so they may be tapping into part of the pathway required to maintain the stems cells while suppressing xylem differentiation to form a structure that serves as a nutrient sink,” Mitchum said. “To me that’s really cool.”

This means these cells are free to serve the nematode. Many of their cell walls dissolve to create a large nutrient storage container for the nematode and some create finger-like cell wall ingrowths that increase the take up of food being piped through the roots. For a nematode, that’s a lifetime of meals for it while it sits immobile, just eating.

But how did scientists figure out and test that this nematode’s chemical was the cause?

Using next generation sequencing technologies that were previously unavailable, Michael Gardner, a graduate research assistant, and Jianying Wang, a senior research associate in Mitchum’s lab, compared the pieces of the plant and nematode genome and found nearly identical peptides in both — B-type CLE peptides.

“Everything is faster, more sensitive and we can detect things that had gone undetected through these technological advances that didn’t exist 10 years ago,” Mitchum said.

To test their theory, Xiaoli Guo, postdoctoral researcher and first author of the study in Mitchum’s lab synthesized the B-type CLE nematode peptide and applied it to vascular stem cells of the model plant Arabidopsis. They found that the nematode peptides triggered a growth response in much the same way as the plants own peptides affected development.

They used mutant Arabidopsis plants engineered to not be affected as much by this peptide to confirm their findings.

“We knocked out genes in the plant to turn off this pathway, and that caused the nematode’s feeding cell to be compromised. That’s why you see reduced development of the nematode on the plants.”

This all matters because these tiny nematodes cost U.S. farmers billions every year in lost yields from soybeans, and similar nematodes affect sugar beets, potatoes, corn and other crops.

While this discovery is just a piece of a puzzle, these pieces hopefully will come together to build better crops.

“You have to know what is happening before you can intervene,” Mitchum said. “Now our biggest hurdle is to figure out how to not compromise plant growth while blocking only the nematode’s version of this peptide.”

Mitchum is a Bond LSC investigator and an associate professor of Plant Sciences in the College of Agriculture, Food and Natural Resources. The study “Identification of cyst nematode B-type CLE peptides and modulation of the vascular stem cell pathway for feeding cell formation” recently was published by the journal PLOS Pathogens in February 2017.