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Ghana Challa, a Postdoc on the Crops in silico (Cis) team and member of Principal Investigator Amy Marshall-Colón’s lab at the University of Illinois at Urbana-Champaign, has an incredible vision for the future of farming.

“My vision is this: In 10 or 20 years, there will be an app for farmers where you can plug in all the variables like precipitation, climate, soil fertility — everything — and the app will help you choose the most optimal variety of crops to grow.”

Challa grew up in Andhra Pradesh, a state that’s often called “the rice bowl of India.”

“When we were kids, every summer we used to go to my grandma’s place, and we’d play in the fields,” he said.

Surrounded by crops, he became interested in finding ways to better the plants that feed us.

“At my home, we used to have a small garden, and I used to play with the plants,” he recalled. “Even when I was a kid, my mom says that I was happier playing in the dirt than anything else. Her belief is that any plant I put in the soil will grow into a good plant.”

Challa’s fascination with crops led him to pursue an M.S. in Biotechnology at Andhra University. Looking to continue his research, Challa moved to the U.S. in 2010 to get his Ph.D. in Biology at South Dakota State University. His dissertation focused on wheat and soybeans, which he studied using a combination of old-school and new-school genetics.

“I started as a bench scientist, or an experimental biologist looking at genetics and phenotypes. I moved to computational biology using large scale datasets and high-performance computing, coding, and writing scripts to analyze the data to understand the biology behind the phenotypes.”

For Challa, computational biology offers a unique shift in perspective, and an opportunity to understand plants on multiple scales and levels of complexity.

“I’m always interested in looking at the big picture, kind of like zooming in and out to understand what’s happening in the plant. Most of the research that’s out there focuses on just one thing, like one gene or one pathway. You’ll get a lot of information from that, but after that, you must zoom out and look at the larger picture, and you’ll see some important connections. It’s like focusing a camera until you get the whole picture.”

Pursuing his passion for computational biology, Challa moved to Urbana-Champaign for his postdoctoral research in May 2018.

Challa now works for Marshall-Colón, an Assistant Professor of Plant Biology, as part of the Crops in silico 2.0 team. Crops in silico 2.0 is a $5 million project funded by the Foundation for Food and Agriculture Research, which aims to use computational modeling to better understand how crops will respond in the face of changing climate conditions. Crops in silico’s flagship crops — maize, soybeans, sorghum, and wheat — account for about 60% of all the calories we consume. A better understanding of these crops and how they respond to different environmental conditions is necessary to address current and future food insecurity.

“The Marshall-Colón Lab is a systems biology lab, so we try to look at the big picture,” Challa said. “Not just looking at only the gene expression, or only how the proteins work, or only the chemicals the plant makes — we want to put everything into one connected model.”

He describes it as being “like a video game.” That is to say, you change one small parameter, such as soil acidity, and then the model shows you how the plant responds, from changes at the molecular level all the way up to changes in the crop’s yield.

“The basic principle of life is that you have DNA that makes RNA, and RNA has the information for making proteins, and proteins do the work necessary for the cell to sustain itself,” Challa explained. “Much of the past research has either focused solely on differences in DNA sequence, solely on differences in mRNA abundance, or solely on differences in protein abundance and/or activity, but not all at the same time.”

Challa’s work focuses on analyzing gene expression, modelling gene regulation networks, and connecting them to plant-scale metabolic models. To make his models work, he needs parameters — data collected from the field that will ensure the models accurately emulate plant function.

“Just the other day we were out in the field collecting photosynthesis and gas exchange data,” he said. “That helps us put in the values needed for the models to work.”

So far, Challa has set up a computational pipeline for the Crops in silico project, which analyzes high-throughput sequencing data. In the future, he plans to optimize the model for different crops, so that there will be a unified pipeline, allowing data to be exchanged more easily.

Massive amounts of crop data are needed to construct these models. As such, the lab supplements its own data with data collected by other researchers: “It’s all about teamwork,” Challa said. “We cannot do everything on our own.”

In fact, teamwork is a driving force behind the Crops in silico project. For Challa, the best part of being involved with Cis is getting to work with researchers from many different fields, including astronomy, math, and remote sensing.

“If you talk to others from different fields about your work, maybe they have a different perspective, and they can give you suggestions,” he said. “That’s how I want my research to be. Learning from others and helping others.”

In addition to Cis, Challa also works for Marshall-Colón and Crop Sciences Professor Matthew Hudson on energy crops as part of the Feedstock Production Theme at the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI).

Outside of the lab, Challa continues engaging with his interests. His love for computing started as a hobby: He’s a tinkerer and has even built his own supercomputer. He also grows his own fruits and vegetables using a hydroponics system he built himself.

Challa’s passion for understanding and improving crops is driven by his desire to help create a sustainable future.

“A lot of studies say we have to increase our food production by 40% by 2050 because we have a growing population,” he said. “However, something we often overlook is that in the future, we’ll have less land for food production than we do now, due to sea level rise and changing climate. So we need to produce 40% more food with less land. And to achieve that, we need to find other solutions than just spraying chemicals and using fertilizer.

“That’s one reason I chose to work here. We need to produce more, but at the same time, we need to put less stress on the planet.”

— Article by iSEE Communications Intern April Wendling

Eric Wolske, a member of Illinois’ Agroforestry for Food (A4F) team, has found a simple way to explain the project’s work:

“Agroforestry is growing crops with trees. That is the most basic level.”

Originally from the Champaign-Urbana area, Wolske decided to go to Southern Illinois University in Carbondale for his B.S. in Plant and Soil Science. That campus’ main quad is a forest, which was a big draw for Wolske. His college experience felt like trees were more than just campus décor.

“At the time I was more interested in booze crops: grapes, cider apples, all that fun stuff,” he said.

After earning his undergraduate degree, Wolske spent time working in a vineyard — Southern Illinois has a lot of these.

“I’m from the fruit side; I think even fruits could be more sustainable,” he said. “They’re already in a sustainable category. They’re perennials, they stay there. There’s a fairly low amount of tillage, but it just seems like there’s still a pretty big gap between getting all the potential ecosystems services and protecting your soil and everything else.”

His interest in sustainable agriculture eventually brought Wolske to the Urbana-Champaign campus. A huge reason that Wolske decided to come home for the Crop Sciences M.S. and Ph.D. programs here was the A4F project, seed-funded by the Institute for Sustainability, Energy, and Environment (iSEE), which is pursuing alternative agriculture options in the Midwest.

Wolske’s master’s thesis focused on shade tolerance of black currants, a woody shrub that produces edible berries. This work transferred into Wolske’s Ph.D. research, where he is now testing shade tolerance across 24 species of currants.

“We’re just trying to see, is (shade tolerance) just in general that as a species it’s something they’re good at? Or are there traits that some varieties have that others don’t?” he said. “How can we help them perform better under shade?”

This passion for the environment and polyculture systems is evident when touring the experimental fields that Wolske has worked over the years. Every element used in experimentation was handmade, crafted, and recrafted (when the Illinois winds had other plans for his canopies).

“A ton of research still needs to be done to see if these systems have potential,” he said. “We’re starting to see, well they work this way, they don’t work this way. We’re puzzling it all out. And what we’re doing here is just scratching the surface.”

Walking through fields, you can see just how much agroforestry is trying to integrate diversity back into the environment.

Right now, the A4F team works with a variety of plants — from peaches and raspberries to hazelnuts and chestnuts. But Wolske said all these crops share a common theme:

“They’re natives, or they can be natives. The chestnuts have a high carbohydrate to them, which is pretty similar to what corn has, which is why corn is grown all over the place.”

Similarly, hazelnuts could serve as a substitute for the abundant soybean production in Illinois. They are high in oil, which is what makes soybeans so prized in production. Still, finding a balance between native and hybrid is something the team is working toward.

“Current natives, chestnuts, have a disease,” Wolske said. “The American chestnut doesn’t do too well. We have a lot of hybrids out there either with Chinese chestnut or the European chestnuts.

“The hazelnut, we have mostly native hazelnuts down there. But they’re not quite the quality that you might get from European hazelnuts. That’s your Nutella.”

Planting native species could be commercially successful and a more sustainable agriculture option. Wolske’s day-to-day projects vary just as greatly as the crops that agroforestry produces in the fields. And much like the crops, Wolske’s work changes with the season.

Starting in the early spring, pruning is the first task.

“That switches over to getting a lot of the experiments all set up,” he said. “Then we have all the field work and everything else, like harvest times. And then I’ll go into the lab and do a bunch of chemical assays on the berries and everything else. And then I’ll go back into the writing period.”

The perennial side of the A4F project is another factor that Wolske enjoys: “I don’t like planting stuff every year, so stuff you just plant and let it go and you take care of them after that is way more my style.”

This didn’t stop him from trying to plant his own home garden — though with all the work he does with the agroforestry project, he quickly found he just didn’t have the time for regular maintenance.

“I had two plots about 30×30 feet, and it slowly turned into a giant chunk of weeds,” he said. “I was growing mare’s tail, goldenrod, which ended up being a great pollinator strip.”

Now, Wolske helps to maintain other people’s gardens. Regularly, he will prune community gardens that have the crops he knows and loves — grapes — among others. Though now with his new pointer hound mix, Ponyo, Wolske has a great distraction from the daily work of his Ph.D. projects.

In the future, Wolske hopes to continue his work with perennials and polycultures. He enjoys the research side of the project, but there is still a lot outside of research that Wolske would like to pursue.

“Teaching would be nice. Or maybe having my own winery someday would be pretty cool, too,” he said.

In the meantime, he will continue his A4F work, watching the farm he helped plant on his first day on the job continue to grow and evolve.

— Article by Taylor Jennings, iSEE Communications Intern; photos by Jordan Goebig, iSEE Communications Specialist

 

AJ Christensen has always wanted to use his computer science and graphic design talents in service of a worthy cause. Now, as a programmer in Illinois’ Advanced Visualization Lab (AVL) and a member of the Crops in silico research team, his visualizations appear on screens big and small to educate, entertain, and empower audiences around the world.

From the moment Christensen first set foot on campus as an undergrad, he felt at home at the University of Illinois and in the Champaign-Urbana community. Originally, Christensen aimed to leverage his B.S. in Computer Science (CS) toward a career in character animation.

“When I was an undergraduate, my goal was to work for Pixar, but I think at the time I didn’t realize that there wasn’t a very clear path between CS and character animation,” he said.

Christensen’s interest in filmmaking led to a semester abroad at Griffith Film School in Australia, a unique experience — albeit atypical for a CS major — which added to his “whole weird mishmash of a background.”

The character animation path might not have been in the cards for Christensen, but it nonetheless opened doors into his chosen field. A collaborative animation project with Donna Cox at the National Center for Supercomputing Applications led to his role in the AVL, which he began upon graduating.

“I was exposed to what scientific visualization was — how it leveraged my animation skills but was more relevant to a CS background,” he said. “Joining the AVL team was a dream combination of my science background, programming background, and interest in movie-making.”

At the AVL, Christensen uses supercomputer-generated data to develop visuals — mostly 3D computer graphics — that appear in media like TV shows, planetarium dome presentations, and Hollywood films. In 2014, he took a leave of absence to work on a particularly high-profile film: Interstellar. Christensen’s role with London-based studio Double Negative involved working with a team to design the visualization for the film’s trademark black hole scene.

“It was useful to see the ways in which the scientific and visual effects communities feed off of each other. Science can’t be done without storytelling, and the techniques that storytellers use are heavily based on what’s been developed in scientific communities,” Christensen said.

Now approaching his 10th year with the AVL, Christensen’s favorite project with the team will always be his first film: Hubble 3D. This IMAX movie about the Hubble telescope provided opportunities for Christensen’s team to mingle with astronauts, scientists, and film gurus alike.

“The rest of the team might say it was more exhausting than exciting, but for me, coming out of school and used to working all night long, it was thrilling to be working on a real Hollywood production,” he said.

Silver screen projects aside, Christensen loves that his role in the AVL’s “Renaissance team” is an education-focused environment that encourages him to try on as many scientific and artistic hats as he wants. This often involves returning to his character animation roots.

“I ride the line between programmer and artist, but sometimes I’ll swing wide and start writing software, and sometimes I’ll swing wide and animate a little character piece, depending on what the project is,” he said.

Another of Christensen’s favorite NCSA projects is his partnership with the Crops in silico (Cis) program, initially seed-funded by the Institute for Sustainability, Energy, and Environment (iSEE). The initiative, literally named “Crops in computers,” is revolutionizing agricultural sustainability by augmenting field trials with virtual crop experimentation. As a visualization programmer on the Cis team, Christensen is responsible for crafting digital models of real crops.

“Crops in silico has been an exciting opportunity to explore visualization from another perspective. We’ve gotten experience with simulations of astronomy, geology, and biology, but crop science is a completely different animal. This could be — and has been — groundbreaking. It’s totally new, totally unseen. And it’s exciting to be there at the beginning,” he said.

Recently, Christensen collaborated with a crop scientist to simulate soybeans for a research project about photosynthesis. After a crop of soybeans was cultivated and the measurements were recorded, Christensen leveraged the collected data to generate hundreds of true-to-life virtual versions of the plants. The computer-generated crops could then be exposed to simulated sunlight, with the observations accurately reflecting what would happen if those plants were grown in the field.

Experiments executed in silico not only occur at an accelerated pace, but can be manipulated to reflect future scenarios as well as current conditions. Barring the invention of a time machine, this is an invaluable and never-before-seen capability.

“We’re experimenting with digital crops quickly so that we can understand how crops might grow in future climates, including climates that don’t exist on the planet right now. When those climates begin to affect life on Earth, we will have knowledge that will contribute to the quality of food that we need,” he said.

Working on the Cis team not only engages Christensen’s passion for programming, but his love for public service as well. Specifically: science communication, educational outreach, and informing the public about complex topics with compassion and empathy.

“It plays into my passion for science communication and my passion for helping people understand. One of our concerns these days is that there’s a lot of anti-science rhetoric out there, and trying to understand how to break through that, and do science communication better, is really important,” he said.

While Christensen’s goal is to communicate science to the general public, Crops in silico has also affected his own personal outlook on what it means to be a positive change-maker:

“One of the reasons I’m excited about Cis is the reason that everyone should be excited about it. This is an opportunity to do something that does make a difference, and it’s an optimistic view on how to handle climate change, so I’m empowered by that.”

When asked about the message he hopes to convey with his visualizations — whether they pertain to the solar system, sustainability, or anything in between — Christensen answers:

“It’s not all doom and gloom. There is a future, but we have to work for it.”

— Article and photos by Jenna Kurtzweil, iSEE Communications Intern

 

Sustainability leadership, research, education, and practices will remain at the forefront of University of Illinois priorities, thanks in part to significant endowments from Stuart L. and Nancy J. Levenick of Naples, Fla.

Mr. Levenick, a U of I alumnus who captained the 1975 Illini football team and received a B.S. in forestry in 1976, and his wife have designated this major endowment in two parts:

• for the Stuart L. and Nancy J. Levenick Sustainability Chair Fund, which will establish an endowed chair in the College of Agricultural, Consumer and Environmental Sciences’ Department of Natural Resources and Environmental Sciences (NRES); and
• for the Stuart L. and Nancy J. Levenick Resident Scholars in Sustainability Leadership Program Fund, to establish a resident scholars program at the Institute for Sustainability, Energy, and Environment (iSEE).

“As a forestry major on this campus, I learned the value of a strong, resilient environment and humanity’s place in nurturing it,” said Mr. Levenick, a former executive at Caterpillar Inc. and a longtime resident of Peoria. “As a growing world population must address its increasing food, clean water, energy, shelter, and basic health needs — without doing damage to the environment — we need leaders to emerge. New critical thinking is needed to address these challenges.

“Nancy and I hope that our funding can play a role by establishing a thought leadership program at Illinois that will benefit future generations.”

NRES will select a faculty member to serve as the Levenick Chair in Sustainability. As an iSEE affiliate, this newly funded Chair will also recruit and manage the Resident Scholars Program at the Institute.

“We are excited about the impact the Levenick Chair in Sustainability will have for our department,” NRES Head Jeffrey Brawn said. “As the first endowed chair in NRES, it will create stability and drive excellence in environmental sustainability research and instruction.

“As the chair brings together experts worldwide to collaboratively inform translational research, the University and society will also benefit. This gift helps to ensure we continue to bring the best and brightest leaders in environmental sustainability to Illinois — today and for many years to come.”

The Levenick Resident Scholars in Sustainability Leadership Program at iSEE will bring in experts from other universities, the private sector, and nonprofit organizations to share fresh perspectives and innovations with the Illinois community.

“Stu and Nancy have again helped advance iSEE’s mission with their incredible support,” said Evan H. DeLucia, the Institute’s Baum Family Director. “Their previous generosity in funding a research and educational fellowship program was an integral part of our efforts toward researching real-world solutions to sustainability, energy, and environmental issues. It has helped Illinois students learn to be sustainability-minded on campus, in the work force, and as future community leaders.”

With backgrounds from a variety of disciplines, the new Resident Scholars will enhance and accelerate the broader impact of sustainability research and innovation, he said. As the Levenick Chair leads the program, it will help “close the circle” on sustainability efforts already established among the College of ACES, iSEE, and NRES.

“This campus will become a destination for worldwide sustainability experts — offering them creative opportunities and exposing faculty, students, and staff on our campus to real-time sustainability solutions from across the globe,” DeLucia said.

This is not the first time the Levenicks have shown their generosity to Illinois. In 2015, their gift allowed creation of the Levenick iSEE Fellows Program, funding faculty and student research as well as faculty instructors for courses in the campuswide minor led by the Institute. A partial match in 2016 from Mr. Levenick’s former employer Caterpillar helped fund the iSEE Collaboratory, which opened in January 2019 and features a cutting-edge i-Flex classroom/meeting space/teleconferencing area, as well as a media studio. Current Fellows are using this space, and it will become a meeting and creative space for the Resident Scholars.

In addition, the Levenicks have donated to the U of I’s Division of Intercollegiate Athletics. In 2018 as part of the University’s $2.25 billion fundraising campaign, With Illinois, they provided a significant gift toward the football team’s new performance center that will house a weight room, coaches’ offices, meeting rooms, locker rooms, a two-lane bowling alley, a barbershop, and the Levenick Auditorium. The Levenicks had previously endowed a scholarship fund for walk-on football players.

Mr. Levenick, a former walk-on with the Illini, went on to become an All-Big Ten selection and a 1976 NFL draftee by the Baltimore Colts.

— Tony Mancuso, iSEE Communications and Public Affairs Director

“From an early age, I was aware of farming going on around me, and the importance of land and soil to everything in our lives.”

Originally from Sacramento, a vibrant city nestled at the top of California’s Central Valley, iSEE Postdoctoral Research Associate Ilsa Kantola grew up surrounded by agriculture both geographically and genetically — Kantola’s grandfathers worked in the industry, and her father has a degree in Agricultural Economics. Living in a bustling metropolis did nothing to hinder Kantola’s bond with nature; on the contrary, she fondly recalls driving down country roads playing a game called “Name that Crop.”

“Which,” Kantola jokes, “can be a very boring game in Illinois.”

In her work at the University of Illinois at Urbana-Champaign, Kantola contributes to the industry’s most high-stakes conversation: the search for sustainable farming practices of global proportions.

Kantola has long been passionate about her current field: her bachelor’s degree from California Polytechnic State University is in Environmental Engineering with a Soil Science minor. Soil Science quickly developed into a central interest area — and influenced Kantola’s decision to complete her Ph.D. at Texas A&M in the department of Rangeland Ecology and Management, now Ecosystem Science and Management.

The decision to study soil in Texas was not a difficult one.

“It’s chemistry, it’s biology, it’s agriculture, it’s food, and it’s people,” Kantola says of her passion for the subject. “And it’s all together.”

While in Texas, she studied the methods by which woody plant invasion transforms south Texas grasslands into shrublands, with a focus on the behavior of soil-bound carbon, nitrogen, and phosphorus — her “trio of interests.”

“I worked in rangelands,” Kantola says of her department’s name, “but I did not work with cattle — I worked with the land they had taken cattle out of.”

When Kantola arrived at Illinois to work for the Energy Biosciences Institute (EBI), her focus shifted from Texas grasslands to Midwest croplands. Her team’s BP-funded study sought corn alternatives for the production of bioethanol — a naturally produced fuel supplement — and her objective was to measure the ecological effects of using perennial grasses as a substitute.

Native switchgrass and the Asian hybrid Miscanthus x giganteus grown at the Illinois Energy Farm were posited as promising alternatives because perennials — plants with life cycles longer than one growing season — require less management than annuals such as corn, with potential for similar or greater yields. Additionally, the Miscanthus variety grown at the Energy Farm cannot be consumed by humans or livestock, so bioethanol production would not come at the cost of a viable food source.

Kantola expresses a passion for using focused research to drive big results:

“We start small, digging at the farm. But U of I sites are representative of the larger Midwest, so data we collect can be scaled up to visualize what’s happening on a larger scale.”

Passion for the big picture informs Kantola’s current research at Illinois in partnership with the Leverhulme Centre for Climate Change Mitigation (LC3M). The project, led by iSEE Director Evan H. DeLucia and and Plant Biology and Crop Sciences Associate Professor Carl Bernacchi, aims to combat rising atmospheric carbon dioxide (CO₂) levels by imbuing cropland soil with calcium- and magnesium-containing silicate rocks.

The researchers’ process for capturing atmospheric CO₂ involves two chemical reactions. First, atmospheric CO₂ dissolves in rainwater to create carbonic acid. Then, the acid reacts with calcium and magnesium in the soil to form calcium and magnesium bicarbonate, soluble compounds that leach with soil water, resulting in the relocation of CO₂ from the atmosphere to the water cycle.

To enhance this process, Kantola’s team turns to basalt, an igneous rock containing both calcium and magnesium as well as phosphorus and minor nutrients that can benefit soil fertility. Large quantities of finely-ground basalt are spread over twin fields of corn and miscanthus at the Energy Farm and left to react with CO₂-laden rainwater.

“We’re trapping atmospheric CO₂ in the water cycle so that it can move out through the drainage tiles, into the Mississippi, down to the Gulf, and potentially benefit the oceans. That’s the dream: that we can cure ocean acidification, reduce atmospheric CO₂, and benefit our crops at the same time.”

Because of basalt composition and soil fertility variation across climates and continents — and the potential for plants and soil microbes to change the rates of basalt weathering — LC3M collects data from three ecologically diverse locations. In addition to the temperate Midwest, basalt is similarly applied to a palm oil plantation in Borneo and a sugarcane field at James Cook University in Queensland, Australia.

“The project is getting global,” Kantola explains. “That was always the intention.”

Looking ahead, Kantola is excited by the prospect of data analysis. This might be several years away; Illinois researchers are currently in year two of a five-year basalt application program. Because basalt is slow-weathering, the initial application period is followed by five years of observation, during which annual yield and biofuel production data will be measured against control fields.

The sooner data is available, the sooner Kantola’s team can make informed recommendations to farmers and spark a chain reaction toward sustainable land management that reaches out into the atmosphere, the oceans, and beyond.

Kantola calls the project’s benefits a “double return:” “It’s a way to use land that’s already in production for biofuel to make an impact on the planet’s atmospheric health.”

Ideally, this project provides the scaffolding for a novel way to address one of the world’s most pressing issues while enhancing—rather than disrupting—traditional farming practices.

“We’re interested in disrupting some things that humans do to the Earth,” Kantola clarifies. “But if we can do so in a way that’s beneficial to food production and CO₂ reduction, that would be the dream.”

— iSEE Communications Intern Jenna Kurzweil