David Mendoza-Cozatl

BIPS: A Semester in Review

May 17, 2021 By Becca Wolf in Research Tags: BIPS, computer science, plant science

Maria Lusardi showing how she connects the pH sensors to the Arduino. | photo by Becca Wolf, Bond LSC

By Becca Wolf | Bond LSC

As the semester comes to an end, Bioinformatics in Plant Sciences (BIPS) close the school year with a lot of accomplishments: one team earned Best Abstract honors at the Mizzou Undergraduate Research Forum, three teams have papers in the review process, one team got their research published in a journal, and two BIPS members were even selected to share their work at the Research Day in Jefferson City, MO.

These teams did not get to these places on their own.

BIPS is in its 3^rd year at Bond Life Sciences Center as an undergraduate program that pairs a plant sciences or biology student with a computer science or engineering student. Most students come in with little to no knowledge on the other’s major but are committed to work together on a project that requires both disciplines.

“I liked how I was able to work with Maria who has different experiences and knowledge than what I do and to be able to work together to create this cohesive project that we’ve been working on all semester. It’s been really rewarding,” Emily Walter said.

Walter, a plant sciences major, worked in the David Mendoza lab at Bond LSC this semester with Maria Lusardi, a computer sciences major.

They focused on using pH sensors with maize grown in a hydroponic system to track the acidification of the root environment when plants were grown with different nutrient availability. Lusardi first worked on tuning the remote pH sensors while Walter established the right hydroponic conditions for maize.

“I’ve been working with a lot of different things. I started out looking at Python [coding language] a lot and trying to get different Python scripts to work, but at the end I worked more with data analysis,” Lusardi said. “I tried to learn a new language so that I could make some applications that would make it easier for us to look at our data.”

They presented their research in Mizzou’s spring Undergraduate Research Forum. The forum was held online this year.

“The presentation talks mostly about the different brands of sensors we used and compared in the experiment and the different data sets,” Lusardi said. “It was more focused on the set up of the plants themselves.”

Walter and Lusardi received a Best Abstract award at the forum.

“It was really cool because I was watching the closing ceremonies and then they said our names. I was surprised, I wasn’t expecting to actually win and be a part of the top best abstracts,” Walter said.

Walter credits BIPS for helping her and Lusardi be comfortable presenting their research poster. The two presented in front of members of BIPS before the forum and received critiques.

“It was nice to know what to improve upon. It was also cool to see what other people were working on and learn about other projects,” Walter said. “I definitely expect to be doing similar stuff like this and hopefully will present live in the future.”

This success is the ultimate goal of BIPS.

“I think it’s very rewarding because you see them at the beginning when they have no idea what the project is,” Mendoza said. “At the beginning, they start by just following instructions, but, little by little, they start getting an understanding of what they are trying to do and start doing things by themselves.”

Mendoza was the principal investigator who initiated BIPS through a National Science Foundation grant.

“We now know the recipe for success, and we want to keep the program growing,” Mendoza said.

Both Walter and Lusardi have learned a lot about the other’s major.

“There are different knowledge and skill sets that you learn that you wouldn’t normally do on your own if you’re just a plant sciences or computer sciences major. It’s a good way to see how those interact to create something more,” Walter said.

Mendoza hopes that BIPS can keep this momentum going next year.

“In the end, the hope is that they learned that moving across fields is not impossible and that you can learn from a different field. You don’t have to be isolated in what you thought would be the rest of your career,” Mendoza said.

Beyond counting: computer science partnership helps speed up plant science experiments

May 12, 2021 By Lauren Hines in Research Tags: BIPS, computer science, high-throughput phenotying, plant science

Janlo Robil, graduate student in the Paula McSteen lab, came up with the GrasVIQ project after he finished a project that required him to count hundreds of plant leaf veins. | photo by Lauren Hines, Bond LSC

By Lauren Hines | Bond LSC

It’s not surprising that researchers feel discouraged when pursuing projects that involve plant leaf vein density analysis. Manually counting individual leaf veins and measuring their density to understand how nutrients are transported in plants can take weeks of tedious work.

That’s how Janlo Robil was feeling when he was working on a maize leaf project while rotating through the Paula McSteen lab in 2016 in Bond LSC.

Now, researchers can cut that time down to just minutes.

As part of the Bioinformatics in Plant Sciences (BIPS) program, undergraduate and graduate students in plant sciences and computer science have come together to create the first phenotype image analysis system for monocot plant leaf veins called, GrasVIQ.

The GrasVIQ software can process photos of grass leaves, automatically detect and count vertical grass leaf veins and calculate various quantitative measurements such as vein density, width and separation. These measurements help analyze leaf vein network patterns.

“The time that you use for collecting data, you can already use for analysis,” said Janlo Robil, head of the project and graduate student in the McSteen lab. “It will also help you in your decision about the direction of your research because the faster you get the data, then the better idea you have if you still need to pursue this or not.”

The project was spurred by Robil in 2017 when he went to a seminar by Filiz Bunyak, assistant research professor in the Electrical Engineering and Computer Science Department.

Bunyak was presenting her group’s interdisciplinary image processing and computer vision research, including their work on plant phenotype analysis. Robil got the idea to apply it to plant leaf veins.

“It started from a simple question,” said Ke Gao, co-author and graduate student in the Electrical Engineering and Computer Science Department. “Can we help them do their analysis faster with repeatable quantified results? We were hopeful we could use our previous experiences in plant image analysis to help Janlo and his lab conduct their analysis more efficiently.”

However, the project was on hold until 2019. Robil simply didn’t have the time or manpower for this project until he heard about the BIPS program.

“I think [the BIPS program is] a very good way of promoting interdisciplinarity in research,” Robil said. “Had I not asked the computer science people to collaborate with me, I would still be manually counting veins right now, and not using software to quantify veins more quickly. I think interdisciplinarity can move science forward and faster, literally.”

The software can identify the vertical veins with 95% accuracy and 92% accuracy for transverse veins when compared to the manual quantification.

“Without any doubt, we believe that the software can do a better job by just the rate of it,” Robil said.

The GrasVIQ phenotyping image analysis software can classify and quantify stained veins of grass and corn leaves. doi.org/10.1111/tpj.15299

While the software saves plant science researchers time and energy, it also provides computer science students something as well.

“Collaborating with plant scientists gives us the opportunity to leverage our expertise in engineering, algorithm development, and mathematical models to contribute to the solution of a real-world problem,” Gao said.

BIPS pairs undergraduate and graduate students from plant sciences and computer science together to work on a project. For undergraduate Claire Neighbors in the McSteen lab and computer science undergraduate Michael Boeding, this was their first published paper.

“It’s super exciting,” Neighbors said. “It feels good like all my hard work meant something.”

Neighbors was the one who had to create the images and do the manual counting to compare to the software’s counting. She said the process took her months.

“It was worth something so that we could make this software valid,” Neighbors said. “Someone had to put in the hours to be able to make those ground truths to show that this software works. So, it feels really good that I was able to contribute something.”

While the software has much to offer, the researchers believe it could be better. Robil thinks vein classification can be improved using machine learning even though the software achieves a detection accuracy of more than 90% for vertical veins.

The current software is designed to be used by scientists and does not have a very friendly user interface. Building a better user interface and further improving the analytics using machine learning approaches are future goals for Gao. GrasVIQ will enable generations of training data for these machine learning-based improvements.

Nonetheless, the software provides an escape from endlessly counting veins.

“We learned how to quantify the veins quickly, but like a year from now, that isn’t going to be what’s taking us months to do,” Neighbors said. “It’s going to be figuring out why this gene made the veins look weird or produced less or thinner, thicker, which is going to make things more efficient in the future.”

More information about the project can be found in, “GrasVIQ: An Image Analysis Framework for Automatically Quantifying Vein Number and Morphology in Grass Leaves.” The paper was published on April 29 in The Plant Journal. The study was done by Janlo Robil, Ke Gao, Claire Neighbors, Michael Boeding, Francine Carland, Filiz Bunyak and Paula McSteen. The Bioinformatics and Plant Sciences (BIPS) program is funded under the National Science Foundation, Cellular Dynamics and Function MCB-1818312 to David Mendoza-Cozatl (University of Missouri, Columbia).

BIPS: Bringing Plant Science and Engineering Together

February 3, 2021 By Becca Wolf in Research Tags: bioinformatics, BIPS, computer science, plant science

Nick Dietz and Marianne Slaten observing a plant in the lab. | photo by Becca Wolf, Bond LSC

By Becca Wolf | Bond LSC

Technology advancements have always driven scientific discoveries in order to perform in depth research, but that has never been more true today.

“A couple of decades ago it was perfectly fine to be an engineer and a biologist and live in your own world,” David Mendoza said. “But as science has advanced, we depend more on mathematics and computer sciences now.”

Mendoza, principal investigator at Bond Life Sciences Center and associate professor of plant sciences, created a program to help develop those skill in the next generation of scientists.

Bioinformatics in Plant Sciences (BIPS) was born in 2016. The undergraduate program pairs plant science or biology majors with computer science or engineering majors. Through research, field trips, and journal clubs, undergraduate students learn how to collaborate on projects and how the two fields help each other.

While Mendoza is the PI who initiated BIPS through a NSF grant, students from all labs are welcome in this program. More recently, a second NSF grant in collaboration with Gary Stacey has allowed the program to expand. BIPS identifies labs that have projects with both computer and biology components for students to work on. Students can also come to BIPS with a project already in mind.

Graduate Student Mentors

BIPS is run by students, for students, with a handful of graduate student mentors and undergraduate students in the program.

The graduate student mentors run weekly meetings, invite in guest speakers, and organize the journal clubs, which is where students review scientific publications and discuss them. Graduate mentors, Marianne Slaten and Nick Dietz, have enjoyed their time and responsibilities at BIPS.

“We make sure they’re on track and don’t get stuck. We want them to become well-rounded researchers,” Slaten said. “It’s a really novel opportunity to jumpstart the next generation of researchers.”

While BIPS cannot go on a field trip this year or have in-person speakers, Slaten and Dietz have come up with alternatives to keep undergrads engaged.

“We’ve been doing workshops showing different bioinformatics tools that can be used to address different research questions,” Dietz said. “We’re also having them do journal club, which gives them a better understanding of the literature surrounding what they are studying. We’re trying to normalize the experience as much as we can, even though everything’s virtual right now.”

A Bioinformatics in Plant Sciences (BIPS) meeting in progress. | photo courtesy of Nick Dietz, Bond LSC

Undergraduates

Undergrads are put into research teams and begin working.

Many projects start with a biology student cataloguing physical plant traits and a computer science or engineering student creates a way to take images of the plants and organize data and information.

“Some of the files you work with are so big you can’t even open them in Excel, so there’s always room for computational people that really know how to harness all that data,” Slaten said. “The files are just so big that your computer crashes. It takes additional skills to know how to deal with that data.”

While a majority of their projects focus on phenotyping, BIPS is looking to branch out into other areas.

“A big problem in biology right now is big data, which you can’t get through that if you don’t have computer science,” said Maddy Creach, a junior from Walter Gassmann’s lab at Bond LSC. “It’s interesting to see the way computer scientists look at problems and that has definitely made me a better researcher, especially since I know 1,000% more about computer science than I did when I started.”

Creach has found that her two years in BIPS helps her think about new ways to think about research.

“A big thing that I have gotten out of BIPS is how to manage my own project,” Creach said. “It’s on me to communicate with my partner and get stuff done and put work towards it, because no one else going to tell me to do it.”

In addition to working on their research and participating in journal club, the undergraduate students are expected to make a poster each year to present their research either at Life Sciences Week or at the Undergraduate Research Forum. Since the pandemic has limited or canceled these events, the students now submit a video of their work online for others to watch.

BIPS’ Impact

Building research and collaboration skills has helped everyone involved.

“I’m learning as much from them as I’m teaching them, so that’s been really awesome,” Slaten said.

Students also hone their communication skills.

“I didn’t realize being a good mentor is a skill set, it’s something you can cultivate over time,” Dietz said. “Oftentimes as students, we think of mentors as either good or bad, you either have it or you don’t. But it’s actually a skill that you can develop over time and I’ve picked that up since I’ve been helping run the program.”

But all remember it’s a learning process.

“Everyone’s really fun and easygoing, no one is judgmental because there is a range in expertise,” Creach said. “There are no dumb questions.”

BIPS has helped many students become well-rounded in their research abilities and is always looking for more students.

“The world is a big place that is moving at a fast pace, and if they don’t get on the train, they are going to miss it,” Mendoza said. “It’s that simple. There’s so much happening in real time, that if you don’t learn how to integrate technology into your research, you’re going lag behind.”

For more information on BIPS or to apply, contact David Mendoza or go to Bioinformatics in Plants (BIPS).

Connecting the World Through the Cloud

December 3, 2020 By Becca Wolf in Research Tags: bioinformatics, COVID-19, high-throughput phenotying

Maria Clare Lusardi, an undergraduate student in the Mendoza lab, uses the cloud, a program apart of CyVerse. | photo by Becca Wolf, Bond LSC

By Becca Wolf | Bond LSC

Clouds come in many shapes and sizes. Some are big and fluffy, others dark and ominous.

Or, as in David Mendoza’s case, the cloud is a hub of experiment information.

Mendoza, an associate professor of plant sciences and scientist in Bond Life Sciences Center, recently joined the CyVerse, a cyberinfrastructure system used by Mendoza’s lab that acts as and allows his team and collaborators to see data in real time. CyVerse, funded by the National Science Foundation, allows life science researchers to share and store their research data in the cloud.

This sort of system has come in quite handy for Mendoza as the Covid-19 pandemic limited the number of people allowed in a lab last spring, forcing him to look for a better way to work remotely but still together.

“These difficulties make you more creative. Covid-19 is a serious, terrible thing, and I could tell my lab was frustrated because they wanted to continue working, but couldn’t because of the restrictions,” Mendoza said. “We needed this. We started implementing the cloud and the opportunities to keep working and collaborate continued and worked out nicely.”

Mendoza connected the cloud to the robots his lab uses to take photos of experiments. These photos are sent every other hour to the cloud, so Mendoza and collaborators can check in on experiments from anywhere in the world.

To get connected, Mendoza brought in Drew Dahlquist, an undergraduate student, to help.

“As a computer science student, the stuff I’m doing feels very natural, but I didn’t realize how much other areas of science could use it. Before I came on, they were storing all the images just on a laptop in the lab and sending them around on thumb drives, which can be very inefficient,” Dahlquist said. “It’s going to greatly improve what David’s doing in the lab.”

Dahlquist has been transferring Mendoza’s data from the thumb drives to the cloud, a process he plans on being done with by the end of the semester.

“Hopefully, I can start tweaking it a little more to refine it and then just see what other needs pop up in the future,” Dahlquist said.

The Project

The main task benefitting from this new approach is a high-throughput phenotyping project, led by Landon Swartz, an undergraduate student in his lab.

“I was kicked off campus when we had quarantine last semester, so all of my projects stopped suddenly,” Swartz said. “I was just stuck at home doing remote stuff, which was not helpful. So that’s where Drew came in to do the cloud stuff. We realized that this is going to be a regular thing for the next few years and will likely happen again in the future.”

The cloud helps Swartz and Mendoza because instead of waiting a week to see how an experiment is doing, it receives frequent updates, so they can make changes to an experiment in real time instead of after the fact.

This is beneficial when they observe how leaf color changes when over or underexposed to nutrients like iron. This can cause chlorosis — when the leaves turn yellow from lack of iron and die. The cloud allows them to see if chlorosis is occurring at a different rate than they expected. With this information, they can change the parameters and continue the experiment without any issues.

“We are establishing protocols where first thing in the morning the machine is going to send me an email with the first photo of the day and to say that the robots are okay. Then, at night before bed, I’ll get the last picture of the day,” Mendoza said.

The camera used to take photos of experiments in the Mendoza lab. These photos are then sent to the cloud. | photo by Becca Wolf, Bond LSC

Collaboration made Easy

In addition to making experiments more accessible for the Mendoza lab, the cloud allows the lab to easily share data with collaborators.

“We started to realize that having our phenotyping robots be controlled remotely or be able to put our data onto the cloud would be super useful, not just for our lab, but also for labs around the world,” Swartz said. “So, maybe the U.S. goes into quarantine, but we have a sister lab in South Africa that is able to pick up our data where we left off and continue to run experiments for us.”

Having multiple labs look at the data at the same time helps create more ideas and exposes more people to those ideas.

“Our goal is to put the data out there and let more people try different approaches to analyze the data so that all of us as a field, can decide what is the best way to do standardized experiments,” Mendoza said.

Also, with the sister lab on another continent, there are people who can check in on the experiments around the clock.

“For instance, the lab in South Africa can see the data in real time. They can see if we need to change the light, increase the light, or make the night longer, and they could also control the nutrients among other things,” Mendoza said.

The cloud will only help experiments in the future.

“The internet is a great resource to collaborate. It’s not often used like that, but we can put data that we’re getting in the moment into this huge database that anyone across the world can look at. It really changes the whole game of science,” Swartz said. “It’s no longer about who can publish things first, it has really become an everyone’s in it together kind of thing. And that’s where I really would like to see this go, and especially in the next 10 or 20 years.”

While it started because of a pandemic, Mendoza sees it as a useful tool regardless of lab restrictions.

“Now that we’ve seen the possibilities, I don’t think we’re going back just because of the amount of experiments that you can do,” Mendoza said. “We actually plan on building more machines with more sensors, so it’s not going away anytime soon.”

#IAmScience Norma Castro-Guerrero

October 9, 2020 By Becca Wolf in #IAmScience Tags: Legume, nutrition

By Becca Wolf | Bond LSC

If you like your work, you won’t ever work a day in your life.

That’s the case for Norma Castro-Guerrero, a research scientist in David Mendoza’s lab at Bond Life Sciences Center. Having a good attitude and making the most of everything is something she strives to do.

“I wake up every day and I am already thinking about what I need to do,” Castro-Guerrero said. “Time flies by during the day. I think that’s a way to know that you love what you do.”

She first witnessed this attitude in action from a principal investigator (PI) in her undergraduate studies at the Universidad Nacional Autónoma de México (UNAM) in her hometown of Mexico City, Mexico. This PI soon became an influential role model in Castro-Guerrero’s life.

“She was such a strong woman and full of enthusiasm for science,” Castro-Guerrero said, “She was so supportive, ‘You’re a woman and you will do great, getting the best grades and publishing papers.’ From there, I think it was very natural to me to keep studying and publishing during my Ph.D. and postdoctorate.”

Castro-Guerrero has implemented this enthusiasm in the Mendoza lab, where she oversees research projects and students. As a senior scientist, she trains the students on how to run a successful lab. She knows firsthand how important an encouraging environment can be for student growth.

“What you want to teach them is how important it is to have a healthy environment to achieve their goals. It’s not only teaching them the techniques or basics, it’s also that they feel comfortable and happy in the lab because they will be more efficient,” she said.

The Mendoza lab gives her the opportunity to express this enthusiasm. Castro-Guerrero enjoys the freedom she has to study her own ideas. Everyone is encouraged to make decisions and solve problems they feel are important.

Castro-Guerrero currently focuses on studying micronutrients in legumes like common bean and soybean, crops used in communities that suffer from nutrient deficiencies. She is looking at what mechanisms the legumes are using compared to other crops that make them accumulate more of these elements. Understanding the key factors will be useful to design better crops.

“Some people’s diet depends on these seeds, so improving them is a perfect vehicle to improve their health,” Castro-Guerrero said.

To further this study, Castro-Guerrero and her team have collaborated with people in South Africa and Mexico to improve the well-being of communities. Helping others motivates her, and this project is rewarding in more ways than one.

Aside from science, Castro-Guerrero’s other passion in life is traveling. And here at Bond LSC, she was able to combine these two passions.

In the past several years, Castro-Guerrero was able to travel to Asia and Africa to discuss research the Mendoza lab is working on at symposiums and other events.

“I really enjoy that people notice what we are doing in Missouri. They know that in the middle of United States we’re doing this great science, and they look for collaboration with us,” Castro-Guerrero said. “So, when you go there and they say start dropping names of people in this building [Bond LSC], we know we are in the right place. Being able to see the recognition not only the university but your own building is getting outside the country, I really enjoy that.”

Castro-Guerrero gets as much as she can out of her international science trips. “I know how people work in Mexico and in the United States. There are differences and it’s very enriching to see how other places work. Their dynamics, their strategies, you learn from them. I think it’s neat to be able to interact with other scientific communities,” Castro-Guerrero said.

“In my lab, the students observe you doing this, talking, writing, discussing, and they want to follow you like I did with my PI in the past,” Castro-Guerrero said, “You see them get excited that they’re working on at Bond LSC. And we are happy and proud of that.”

Science has allowed Castro-Guerrero to wake up every day excited about what it will bring. Whether it is supervising students in the lab, conducting research, or traveling around the world, she is ready for anything.

“I love it, I don’t want to do anything else,” Castro-Guerrero said, then pauses, “Except traveling. But traveling the world while doing science is even better.”

#IAmScience Landon Swartz

May 29, 2020 By Lauren Hines in #IAmScience Tags: bioinformatics, computer science

By Lauren Hines | Bond LSC

Landon Swartz, undergraduate student researcher, is motivated by a simple desire — to help others through the power of computer engineering.

Coming from Springfield, Missouri, Swartz decided to go to Mizzou in 2017.

“I chose engineering,” Swartz said. “It fits my idea of solving problems, but also lets me be able to see a benefit to people.”

Swartz got involved in research through the honors college after he talked to David Mendoza, associate professor in plant sciences and Bond LSC investigator. Mendoza was looking for people to help program and build his data collection machines.

“Robotics is right up my alley,” Swartz said.

In the Mendoza lab, Swartz was modeling the robot and programming it to move, take pictures and run diagnostics.

This experience eventually led Swartz to win the summer 2020 Cherng fellowship from the MU honors college. The nine-week research program provides networking and presentation events along with a $1,000 project expense account.

“It feels really great,” Swartz said. “It was really nice to be able to win that because you do have to plan a full project, like, the beginning, middle and end of everything. So, it’s nice to be able to not only plan that out, but to actually get to do it and get the funding and support to do it.”

The fellowship will help Swartz create his own idea for a robot. After seeing the potential of the robot that images root growth in Mendoza’s lab, Swartz wanted to expand it further by adding an automated hydroponic system.

The system will help researchers easily control variables that will affect the plant and watch how physical traits are affected.

“The reason I came up with the idea for hydroponics is because after watching my lab mates try to do hydroponics, it’s a very labor-intensive procedure,” Swartz said. “It’s a very error prone procedure because you have to do everything manually.”

In addition to saving time for researchers, the robot will also potentially help eliminate human bias in research and increase efficiency.

Since Swartz’ project straddles plant biology and engineering, funding can be hard to find.

“If you can’t find that enthusiasm from grants or any other place, you kind of have to figure it out along the way,” Swartz said. “So, this fellowship will help us a lot with kind of establishing more examples of how you can use automated phenotyping.”

When Swartz isn’t working in the lab or going to his computer engineering classes, he can be found practicing bass guitar, playing the trumpet or running the soundboard for a college ministry on campus.

“Whenever I get confronted with a problem, I usually go and practice for a while just because I feel like it opens up another side of my brain,” Swartz said.

Swartz has been playing the trumpet since middle school and the bass guitar since freshman year of college. Swartz sees the importance of his research even in music.

“Seeing where engineering intersects with plant biology and healthcare and going back to music, like audio equipment, things like that, there’s engineering and everything,” Swartz said.

Swartz sees the potential and power of computer engineering and how it can help people and researchers alike. He plans to be in the lab this summer to try and make that potential a reality.

“Knowing you’re going to be a piece in a puzzle to something greater…. that’s what keeps me going,” Swartz said.

The Little Robot That Can

May 13, 2020 By Lauren Hines in Research Tags: bioinformatics, computer science

Root Imaging System — The imaging system helps collect data on the growth of plants. | photo contributed by Samuel McInturf.

By Lauren Hines | Bond LSC

In a corner of the David Mendoza lab, a small machine runs back and forth across a track, taking pictures continuously of plants grown in clear square plates. This machine not only saves time during data collection but also helps the lab track the growth of plants in real time.

After almost five years of development, the Mendoza lab has reached the final stretch in their robotic endeavors. Now, they’re putting the finishing touches on the machine and getting a scientific article together to be submitted in a peer-reviewed journal.

“A few years back, we realized that our phenotyping methods were insufficient to capture subtle changes, things that aren’t just screamingly obvious, and although small, they’re very important,” said Samuel McInturf, a molecular biologist who is part of David Mendoza’s lab. “So, I set out and learned a whole bunch of stuff about robotics.

The project idea came into being in 2015 and transformed itself into a bioengineering senior capstone class where Mendoza, McInturf and many students from bioengineering, computer science and computer engineering worked on creating different prototypes of this idea.

“We are rapidly moving into a phase of a modular revolution, where our older methods, such as phenotyping by eye, aren’t really going to be sufficient,” McInturf said. “So, these machines represent a transition into mechanization or automation of our current methodologies.”

In addition to making the lab more efficient, the machine makes experiments more reliable.

“[The machine] really decreases the bias, decreases human intervention and increases the amount and quality of data that we are gathering,” said David Mendoza, associate professor in plant sciences and Bond LSC investigator.

Another benefit the robot offers to other labs is that it allows undergraduates to do more.

“[Undergrads] did a lot of repetitive tasks, but we are evolving as a society, so now you can teach them to do a lot of different assays and a lot of more complicated, sophisticated things using robotics,” said Ron Mittler, professor of plant sciences and Bond LSC investigator. “So, I look into this as a big advantage, actually.”

Now that the robot has proved effective, the next step is to share it with others. Last summer, McInturf and others flew to Africa to build a version of the robot for the University of the Western Cape in South Africa but wants labs at MU to use their work.

“The idea was to make the machines not just for us but for labs across the world,” said Landon Swartz, an undergraduate student researcher who is part of the project. “I’m hoping to see us be able to get machines out to other labs and just see how it affects their research and how much good can come from it.”

Soon to be one of their first users, Mittler needs the robot to help screen through the 1,000-3,000 plates his lab ends up with that need to be imaged, measured and processed to determine root growth and other parameters

“If you can optimize processes like that, then you can screen a lot of mutants,” Mittler said. “You can do a lot of different things that will take a lot of time and energy, and then you will not have to always spend power or time on data collection…That’s something that a lot of labs would have liked to have, including mine.”

Even though there’s a paper underway and labs are eager to get their own robot, the Mendoza lab isn’t yet finished with the project.

“Feels good to reach a benchmark,” McInturf said. “But there’s still so much more that we can expand upon.”

As of now, this particular machine is used to track the growth of roots and shoots of plants. However, the robot has potential to do even more.

“Now that we’ve developed all of this expertise, it’s relatively simple to add a heat sensitive camera, so we can see how active a plant’s metabolism is,” McInturf said. “Perhaps we could find a way to measure photosynthesis on the fly. Those types of expansions would be much more powerful.”

But for now, the Mendoza lab is busy writing manuscripts, doing proof of concept experiments and updating the software and user interface for the paper, which is scheduled to be submitted for review within the next few weeks.

A NEET Connection

March 2, 2020 By Becca Wolf in Research Tags: Arabidopsis, cancer, reactive oxygen species

Protein is important in balancing iron and reactive oxygen in plant and cancer cells

Arabidopsis growing in Ron Mittler’s lab. | photo by Becca Wolf, Bond LSC

By Becca Wolf | Bond LSC

You might tend to think durability is more of an issue in building a car or engineering a building, but environmental stress makes resilience vital for plants, too.

In the world of understanding and engineering more durable crops, scientists recently identified a protein that’s key to some of that resilience in a neat way. Actually, it’s literally a NEET protein.

Ron Mittler, a Bond Life Sciences Center principal investigator and professor of plant sciences and surgery, is probing the use of the NEET protein to balance iron and reactive oxygen species (ROS) in the chloroplast to make plants stronger and healthier, and it plays a similar role in cancer cells. These proteins belong to a unique family of iron-sulfur (Fe-S) proteins ideally maintaining the proper balance of the heavy metal in and outside of plant cells. Along with several other scientists, Mittler published his most recent plant findings in The Plant Journal last October.

Since NEET proteins regulate both iron and ROS, Mittler teamed up with heavy metal expert David Mendoza, fellow Bond LSC primary investigator and associate professor of plant sciences. Through a Bond LSC Grant for Innovative Collaborative Research, the two started work at the intersection of two labs.

“The main philosophy of Bond LSC is to establish collaborations between researchers to advance the field of whatever sciences that you do,” Mendoza said.

Mittler and Mendoza looked at how NEET impacts iron and ROS, working together to figure out how to make plants more durable. Doing so, they have made a lot of progress in the field and believe that their collaboration has been a good one. Says Mendoza, “It is a very productive collaboration.”

Trays of Arabidopsis in Ron Mittler’s lab. | photo by Becca Wolf, Bond LSC

A Balancing Act

But the work doesn’t stop with plants. Mittler found NEET proteins also play a similar role in cancer cells, regulating the level of iron and potentially toxic ROS compounds. Humans and plants need iron and ROS, but too much of either can be destructive. NEET proteins allow cells to grow and spread quickly which is beneficial for plants, but detrimental for humans when cancers grow out of control. In humans, NEET proteins also play a significant role metabolism related to diabetes and progression of neurodegenerative diseases.

Despite needing both iron and ROS to function, there can be too much of a good thing. To keep iron levels balanced, oxygen is needed. While oxygen on its own is a fairly stable molecule, adding electrons or exciting the present electrons can make the molecule want to react with things around it creating oxidants. Electrons are the negatively charged particles of an atom that keep balance within the cell. When balanced, iron and ROS helps cells grow, but when placed together, the iron turns ROS into hydroxyl radical, an ion that reacts with anything and destroys everything. If not controlled, this desire to bond with things nearby can damage cells and lead to cancer.

Cancer cells like ROS and iron because it enables them to spread quickly and take over more of the body. To stay balanced, NEET proteins are needed.

“These proteins apparently enable the cells to keep high levels of both iron and ROS and to survive,” says Mittler, “So it looks like cancer needs these proteins because if you suppress these proteins or if you target them with drugs, the cancer cells die.”

Sara Zandalinas holding a dying Arabidopsis seedling and a living seedling in Ron Mittler’s lab. | photo by Becca Wolf, Bond LSC

Poisoning the cell

Knowing NEET proteins make cancer and plant cells stronger, Mittler wanted to look at “what happens if they’re not functioning well,” in hopes to understand their function. To test this, Mittler and his collaborators found a way to make the NEET proteins not function. Mittler called this “poisoning the cell.”

“If there is no protein, there’s no life,” he states. “We were able to control when we introduce this protein, and being able to introduce this protein enabled us to actually find out what happened to the cell if this protein goes bad.”

It was found that if the function of this protein is disrupted, the chloroplast is destroyed. Mittler described it as “completely blown to pieces.” The destruction of the chloroplast is caused by too much iron due to a broken NEET protein. Similarly in cancer cells, if there are no NEET proteins, the cells do not spread as quickly and die.

Mittler elaborated, “What we found is that we can target those proteins in cancer, so then we basically destroy the cancer cells.” Currently, NEET proteins are used as markers in the cancer field. Doctors and scientists look for them in order to help diagnose patients and to figure out life expectancy rates. But in the future, doctors hope to use targets these proteins to kill off cancer cells, a treatment that would be less toxic than chemotherapy.

In plants, Mittler has concluded that the NEET protein would make them grow bigger and faster, leading plants to be “more tolerant to stresses because it has the ability to modulate the levels of iron and reactive oxygen.” Findings like these may one day help plants deal with stress like drought and temperature extremes. With humans continuing to contaminate the environment and climate change escalating conditions, Mittler hopes his findings on iron, ROS, and NEET proteins will make plants able to withstand changes better.

“If I can improve the way plants balance reactive oxygen and iron, I can make plants tolerate much more of these bad combinations of stresses even, and maybe even make bigger, stronger, healthier plants.”

Read more about this research in the October 2019 edition of The Plant Journal article “Expression of a dominant‐negative AtNEET‐H89C protein disrupts iron–sulfur metabolism and iron homeostasis in Arabidopsis.”

The Bond LSC Grant for Innovative Collaborative Research program aims to foster inter-laboratory collaboration to make pilot projects that have potential for later federal funding.

Robots and Africa: Tech transfer accelerates data collection

August 16, 2019 By Mariah Cox in Research Tags: Mizzou Research

Unveiling of Sun Bear — Ke Gao and Sam McInturf reveal Sun Bear to presidents and administrators of UWC and MU.

By Mariah Cox | Bond LSC

Fourteen days. That’s how long it took Sam McInturf and Ke Gao to put together a root imaging machine named ‘Sun Bear’ at the University of the Western Cape in South Africa this past June.

The pair, a postdoctoral researcher in the lab of Bond LSC’s David Mendoza and a computer science Ph.D. candidate, brought the automated approach to capturing data on root growth abroad as part of a technology transfer collaboration under the University of Missouri African Education Program (UMSAEP) established by the board of curators in 1985.

The machine, which optimizes data collection of root growth and provides more intuitive data about the factors that stunt or spur growth, allows researchers to focus more time on larger and diverse projects. In many research labs, automation is the way of the future.

“It changes the game. Being able to do everything in a high throughput fashion and being able to test lots of things at once allows us to consider the type of experiments we might conduct differently,” said McInturf. “All of a sudden we have access to the physical capacity to ask new types of questions.”

After touching down in Cape Town, the duo was immediately met with their first obstacle — the tools and building materials they shipped over were tied up in customs. Although McInturf and Gao prepared for obstacles with power conversions and tool availability, they weren’t anticipating broken equipment or problems with electrical wiring and motors.

Over 14 days, the pair spent 10-12 hours in the lab constructing the machine in preparation for its unveiling with presidents and administrators of both UWC and MU. The construction of the machine coincided with a visit by the University of Missouri System President Mun Choi.

“We went over there with a hard deadline of presenting the machine to the presidents of both universities and we needed to be ready then,” said McInturf. “The sum total of all of our efforts resulted in 15 minutes with the presidents where we got to meet with them, and we got to show off what we had built and the plans that we have come up with for further collaboration.”

McInturf has been instrumental in the project since its beginning.

In 2014, the project idea was brought to McInturf by his adviser David Mendoza. Since then, the project has morphed through four major prototypes and has been worked on by students and researchers across multiple disciplines including bioengineering, computer science and computer engineering. In all, students and researchers from the Division of Plant Sciences and the Electrical Engineering & Computer Science Department spent five years developing the blueprint for the interface and the algorithm for the machine.

UM System President Mun Choi observes Sun Bear, a root imaging machine installed at UWC by two MU researchers.

In its beginning stages, the project was part of a bioengineering senior capstone class, and McInturf was the only person working on it in 2017 as he finished his doctoral work.

“We made serious progress starting about two years ago, but we really hit our stride about one year ago in the fall of 2018,” he said.

Gao joined the team about a year ago to help refine an algorithm to process the data. His algorithm recognizes the seed and the root and measures the root growth over time in conjunction with a time stamp.

However, the robot is still undergoing minor tweaks and finishing touches.

“We’re definitely going to be working on the root tracing algorithm for the fall semester. For now, it’s still a prototype. It’s not very optimized and it’s still a little bit slow,” said Gao. “I’ve been working with Sam to make the interface better to show more information like a graph or a table. Right now, we are only measuring the primary root, but there are also a lot of branches on the root. We don’t have an algorithm yet that’s working well for that scenario.”

The robot is currently being used at both UWC and MU to capture detailed information about root growth under a variety of different stresses, conditions and genetic backgrounds. This method of data collection as compared to the traditional methods of manually measuring and recording information is allowing researchers to better understand how different factors affect root growth.

Sun Bear Root Imaging Machine — The Sun Bear root imaging machine is housed in the Mendoza lab of the Bond LSC. The machine was part of a technology transfer between the University of the Western Cape in Cape Town South Africa and MU in June 2019. | photo by Mariah Cox, Bond LSC

“We are interested in characterizing genes by first breaking them and seeing what happens,” said McInturf. “Once we understand what these genes are doing and how they interact together, then we can go on to engineer crops and conduct targeted breeding strategies to allow plants to survive harsh environments.”

The project is part of a cross-campus collaborative named “The Foundry” funded by CAFNR and housed in the LSC which brings together scientists and engineers from varying disciplines to mechanize biology. Other projects currently being worked on by The Foundry include a hyperspectral camera and a leaf imaging robot.

As for McInturf, this project has opened his eyes to a new realm of possibility in his future career path.

“I didn’t think that I could do this kind of work before this project. Not only did it show me that I have the capacity to do it and that it wasn’t so impossible, but it showed me that I could,” said McInturf. “As I move forward to industry or academia my goal is to be working on the interface between mechanization and plant biology, that is kind of my bread and butter at this point.”

UMSAEP was established in 1985 by the University of Missouri Board of Curators to aid South Africans who were disadvantaged by the then-government’s apartheid policies. In June 1986, a formal memorandum of academic cooperation was signed by then UM President C. Peter Magrath and then UWC Rector Jakes Gerwel. This agreement has the distinction of being the first-ever developed between a nonwhite South African university and an American university.

Pumping Iron: Leaves play a larger role in controlling how plants absorb micronutrients

March 14, 2019 By Mariah Cox in Research Tags: David Mendoza

By Mariah Cox | Bond LSC

How do plants take up and use iron?

For David Mendoza, a scientist at Bond Life Sciences Center, it’s not an inconsequential question. He works to decipher the answer in an effort to better fortify the food we eat.

“We need to understand how plants accumulate iron,” Mendoza said. “Iron is really important for plants and for us because iron is a critical part of proteins that help produce energy, especially for plants in photosynthesis. Without iron, plants are sick. Without iron, we get sick.”

His most recent published work further pinpoints where and how a plant senses the amount of iron, focusing on the leaves. Initially, previous researchers believed the iron sensor was in the roots because plants absorb water and nutrients from the ground. Scientists now describe a circuit of sensors in plants where the leaves sense the iron status of the entire plant and tell the roots to continue or stop uptake.

“It’s counterintuitive that plants sense iron in the leaves, but when you think about it, it does make sense,” Mendoza said. “Although the roots are the first tissue in contact with the soil, their sensor is local and can’t control the entire plant. Leaf signals are systemic and can integrate signals from the entire plant to tell the roots the plant status.”

After studying and comparing iron availability in the model plant Arabidopsis using different growth conditions, Mendoza and his team found that the abundance of different proteins, called transporters, were vital. Transporters can move water, nutrients and other molecules within the plant. In the leaves, they found that a lack of one transporter — Oligopeptide Transporter 3 — causes an over-accumulation of iron throughout the plant. Additionally, they found that this transporter mediates a ‘shoot-to-root’ signaling that prevents excess, potentially fatal, iron uptake at the root level.

By moving plants from iron-available conditions to iron-absent conditions, the team tracked the abundance of OPT3 and other genes over time. They found that the responsive genes in the veins of the plants respond quickly to varying levels of iron. Because iron is an extremely reactive metal, and technically a micronutrient, too much can be as bad as too little.

“There has to be a right balance of having the right concentration inside the cells, and how exactly plants achieve this homeostasis is not known,” Mendoza said.

Mendoza predicts he and his team will find several more iron sensors in the roots, leaves and vascular tissues of their plants.

Standing on the shoulders of scientists before him

Mendoza credits the work of researchers before him for providing the toolbox necessary for his research.

“The reason we are where we are right now is because other researchers have found responsive markers for iron deficiency and, over the years, we have found that there are specific markers for roots and for leaves,” Mendoza said. “In the leaves, there are also different markers for different cell types.”

Knowing that there are iron sensing markers in different cell types, Mendoza and his team were able to ask a simple question — which cell responds faster to iron deficiency?

“The toolbox was already there, we just used it to answer this question and we discovered not only the leaves, but the veins are really sensitive to changes in iron deficiency and sufficiency.”

For Mendoza and his team, the challenge lies in the fact that plants don’t like to accumulate iron. They are working to better understand how to convince the plant to safely store more iron in a way that is available for humans.

“The trick in biofortification is to convince the plant to accumulate more iron in available tissues in a safe and bio-available way,” Mendoza said.

However, increasing the amount of iron in plants can have harmful effects if not careful. Mendoza proposes a double strategy to increase iron uptake in plants and express an iron storage mechanism to prevent iron toxicity.

We are what we eat

According to the World Health Organization, 80% of people globally do not have enough iron in their bodies and 30% of people are anemic. Iron is necessary for the body to generate hemoglobin so that red blood cells can carry oxygen to the rest of the body. This is why some people with low iron levels may experience dizziness, weakness and fatigue.

The main contributor to iron deficiency is our diets. Staples such as corn and rice supply a large portion of our calorie intake, however, they don’t have nearly as many nutrients as greens.

In the future, Mendoza also hopes to look into making plants more selective for nutrients even if they are grown in the presence of other toxic elements, such as cadmium or arsenic.

“Plants are one of the very few organisms that can do absolutely everything with raw elements,” Mendoza said. “They can synthesize everything. I want to understand how they are capable of doing that to fortify the food we eat.”

This research was published in the Journal “Plant, Cell & Environment” in March 2018 and was funded by the US National Science Foundation, CAREER, NSF EPSCoR, Department of Energy and the Vietnam Education Foundation Training Program.

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