Decoding Science

A feral past may help chart the future for Brassica vegetables

June 22, 2021 By Roger Meissen in Research

Illustration of wild relative brassica cretica next to modern broccoli, cabbage and kohlrabi — Although Brassica cretica doesn’t look much like cabbage, broccoli or kohlrabi, the wild relative is the closest relation to our modern vegetables and its endurance might show us how to make our vegetable crops more resilient in the future. | Illustration courtesy of Andi Kur

By Roger Meissen | Bond LSC

You might not envision plant scientists as the modern-day Indiana Jones of biology, but University of Missouri researchers have been hot on the hunt for an evolutionary history, looking for clues to the ancestors of our gardens and grocery shelves.

To find the closest wild relative of the wide-ranging plant species Brassica oleracea, Makenzie Mabry and the Chris Pires lab figuratively combed the hills and seashores of Europe, Africa and the Mediterranean to find a long-lost cousin to many of our vegetable staples.

What they found brings together a puzzling past of a species that could provide insight for conservation and breeding efforts for the future of our vegetables.

“These wild relatives — because they are not under cultivation like our crops — have adapted differently and might be better at herbivory defenses or might be more drought tolerant, and knowing where things were domesticated may help identify genes for those traits,” said Mabry, a principal author and recent Mizzou doctoral graduate. “With techniques like CRISPR, we can look at these differences among wild relatives once they’ve been identified using family trees, and then in the future, hopefully, breeders can then move those traits into the plants, which could help our crops dealing with future climate change.”

The Family Bush

The family structure for mustards to cabbages and everything in between is a messy one.

“Charles Darwin really plugged for evolution to be thought of as a tree with branching patterns, but he did say, well, you know, in some cases, maybe it’s really more like a coral or a shrub,” said Pires, principal investigator and co-investigator on this project. “It’s like the branches are all mixed together, and this paper is revealing Brassica as a classic case of this, a very shrubby ancestry. It’s a mess.”

Whether it’s a bush or a coral, the tangle of Brassica oleracea species show a full gambit of diversification.

You have versions of the species that evolved their leaves into staples like cabbage or kale, others where flowers or inflorescences were domesticated into what we eat now as broccoli or cauliflower and even more that put their efforts into underground parts like kohlrabi.

Pires likens this to how modern dogs have diversified into starkly different breeds from Great Dane to chihuahua.

“You got dogs with big heads and ones wagging fluffy tails and others with little-bitty feet, but they are all still the same in that they are all clearly dogs, right?” Pires said. “Just like dogs, Brassica has shown so much plasticity during its domestication, but many still think of each vegetable as distinct branches and that’s obviously not at all what has happened.”

Pinpointing the origin

This path to finding ancestors and relatives of Brassica oleracea requires covering a lot of territory from comparing thousands of genes to scrutinizing ancient texts on cabbage to analyzing trade routes in the Mediterranean Sea.

Recent theories on the origin of Brassica oleracea have ranged from believing there is a single common ancestor to multiple domestication attempts from several ancestors. Despite these hypotheses, it had yet to have been fully confirmed. From England to France to Spain, each region has a certain pride in its favorite varieties of the species. One Greek legend refers to where cabbage sprung from where Zeus’ sweat hit the ground.

The team looked through the literature and archaeological evidence across centuries for these cultural references to gain insight into the origin of the species.

“For some reason, cabbage specifically means a lot to the English, but one of the parts that I think is really cool is that these vegetables have such cultural identities,” Mabry said. “Whether it’s a backyard garden in Portugal or England, there’s a lot of humanity in Brassica oleracea and while understanding that history is complicated, it has such a human component to it that deserves attention.”

The genetics beneath

From a genetic standpoint, Mabry compared 224 different specimens representing 14 crops and nine wild species. After grinding up the leaves in liquid nitrogen and using the Mizzou Genomics Technology Core to sequence transcriptomes (the expressed part of genomes), she then analyzed the DNA from samples that were originally collected all over the world, and then looked for overlapping similarities to understand their shared evolutionary history.

“Just like my mom and I share a set of genes, I can look at the genes in common here. Each sample will have little bits of differences due to mutations, but the more closely related they are the more they share those differences,” Mabry said. “We found Brassica cretica is the closest living wild relative, which grows in the landscape of the eastern Mediterranean region east of Italy. But my favorite part might be we also found that B. cretica has a long history of at least being partially domesticated and then returning to the wild.”

These so-called feral species of former vegetables hold a lot of promise.

“For me, I really love the feral plants. These plants had a different evolutionary history through being cultivated then returning to the wild, now on their own their own path doing their own thing,” Mabry said. “I think it’s really exciting because this subset of plants have even more in common with our crops than wild relatives because they have been domesticated at one time with the same subset of genes. This is under-appreciated gene pool that could really be an exciting avenue for future crop improvement.”

Mabry’s next step is to go in person to these regions in Greece, Crete, Italy, and Morocco to search the hills herself for the ancestors of mustard as part of a National Geographic grant project postponed because of Covid-19.

“I was supposed to go to create and collect these plants in March 2020 and then the pandemic happened, so now that is the next step to figure out,” Mabry said. “My goal is to go next summer once vaccination rollouts around the world play out. We’ll get there soon, and I know the plants will be there waiting.”

This research published June 22, 2021, in the journal Molecular Biology and Evolution, titled “The Evolutionary History of Wild, Domesticated, and Feral Brassica Oleracea.”

New observation from Stacey lab could help advance plant engineering

May 25, 2021 By Lauren Hines in Research Tags: plant science, plant signaling pathways

Large amounts of the Arabidopsis plant are grown at Bond Life Sciences Center for multiple labs to experiment with and use. | photo by Mariah Cox, Bond LSC

By Lauren Hines | Bond LSC

Think about how a home alarm system alerts a person to a potential burglary with sensors detecting whether an intruder picked a lock, came through a window or came through a garage.

Plants are much like this, surviving with the help of their thousands of sensors that can send danger signals to the whole plant so it can react effectively.

“Plants have to have a whole variety of different mechanisms to respond to their environment because they’re stuck in one spot,” said Gary Stacey, principal investigator at Bond Life Sciences Center. “The way they do that is they have all these membrane-associated receptors, and they receive signals from the outside … so they can induce a defense response.”

Stacey’s lab recently made an observation that could lead to interesting future advancements in plant breeding and engineering. Its work was published May 12 in the journal Nature Communications.

The lab found when a lipid — a fatty molecule — is attached to a receptor, a cysteine amino acid within a protein is modified. This process, in turn, makes the receptor silent. The addition of the lipid is called acylation. The lab found that they could also reverse this process and reactivate the receptor.

In other words, this process can turn receptors on and off, which is what tells the plant that there’s danger.

In addition, the lab can use the acylation process to identify the binding protein and, therefore, identify the receptor that is binding to the protein.

“There’s a lot of receptors for which we don’t know the ligand,” said Stacey. “In other words, if you line up all the receptors, there are only a few of which we know what they’re binding to.”

Identifying these receptors’ functions and what these receptors bind to is a high priority in plant research and agriculture communities.

“If we knew all the receptors, say, that responded to drought or if we knew all the receptors that responded to high light or pathogens or whatever there might be in the ozone … then that would open up pathways for us to engineer plants that are more resistant to these stresses, which would make crop production more sustainable, especially in lieu of the changing climate that we have, and would really be a big step forward for agriculture,” Stacey said

According to Stacey, researchers have been able to identify the function of “a small fraction” of receptors out of 2,000 in the model plant, Arabidopsis. However, the Stacey lab is currently developing a way to find these receptors’ functions.

Developing this analysis has been technically difficult so far — needing more funding and manpower to do all the experiments — but the lab is currently in the proofing stage to verify what they know. So far, they can correctly identify the binding protein and the receptor it binds to for some receptors, but it’s less clear for other receptors. More experiments are needed to see if the analysis will work.

“There are 2,000 [receptors], and we only know the function of a handful,” Stacey said. “There’s a lot of stuff that remains to be discovered and a lot of potentials to do something useful.”’

More information about the study can be found in, “S-acylation of P2K1 mediates extracellular ATP-induced immune signaling in Arabidopsis.” Stacey’s lab collaborated with Dongqin Chen, Fengsheng Hao and Huiqi Mu of the State Key Laboratory of Agrobiotechnology in China, Nagib Ahsan of the University of Oklahoma and Jay Thelen at Bond Life Sciences Center.

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.

#IAmScience Kulbir Sandhu

May 14, 2021 By Lauren Hines in #IAmScience Tags: CRISPR, reactive oxygen species

By Lauren Hines | Bond LSC

Kulbir Sandhu’s curiosity had guided him from place to place, but it was his fascination with plant science that has stayed the same.

While Sandhu has been a postdoctoral fellow in the Bing Yang lab at Bond Life Sciences Center for the past six months, his path towards plant science began when he was 18 years old in his home country of India.

In high school, Sandhu was drawn to the biology route because of helpful and enthusiastic science teachers. He grew to like it as time went on and found that the subject came easy to him.

“I always had, you could say, a ‘scientific’ attitude,” Sandhu said. “Even when I had little understanding of the process of science, I always had an attitude that suited this field.”

Sandhu also received support and inspiration regarding science from his father, who was an engineer.

“When I was young, my dad used to help me with school homework,” Sandhu said. “His favorite subject was maths, and so he always insisted that I do well in maths and science. In this way, it became natural for me to develop an inclination for these two subjects. In India, most students interested in science choose either maths or biology streams after 10th grade. Initially, I wanted to be a doctor, so I chose biology, and it was more of a happenstance that I ended up becoming a plant ‘doctor.’”

Years later, Sandhu received his Master’s in plant breeding from the Punjab Agricultural University in Ludhiana, India in 2003, and in 2013 he received his Ph.D. at Washington University.

Sandhu first met Bing Yang four years later as a postdoctoral fellow at Iowa State University. Since they worked on a previous project together, Sandhu became a great addition to the Yang lab when he joined in November last year.

While Sandhu is working on a few projects, his main one involves using the gene-editing tool, CRISPR/CAS9, to target genes in Arabidopsis that code for reactive oxygen species. ROS helps plants with signaling, development, stress responses and other processes.

ROS is also part of the plant’s innate defense system against pathogens. Understanding how pathogens overcome this primary defense system of plants is necessary to breed better resistant crops and reduce environmental impact due to chemical control.

By causing these gene mutations, he prevents ROS from being formed in cells. That way, they can compare the mutant plant to a wild type and see the difference in basal-defense responses.

“Now this is exciting again because we are working in CRISPR in field crops as well as in basic science,” Sandhu said. “So, I get to do both things.”

First-year researcher Jack Ogilvy has been working on this project with Sandhu for the past three months as part of the Freshmen Research in Plants program.

“This is my first time … mentoring someone, and by this experience, I have realized that it is equally beneficial to me,” Sandhu said. “I mean … talking about scientific concepts helps create a deeper understanding, and both parties gain from this interaction.”

Together, the two are learning more about ROS and the Yang lab.

“He cares more about just being a mentor in terms of science,” Ogilvy said. “He also is just as interested in my personal life … We’ve formed a relationship between the two of us where it’s not just like, he tells me what to do in the lab. It’s like we are working together, essentially.”

Ogilvy appreciates Sandhu’s curiosity and advice.

“He’s always telling me to try to find the answer on my own before I go for help to gain that skill … just because it’s such an important skill to have to be somewhat self-reliant,” Ogilvy said. “But that being said, he’s always there if I get stuck or if I need help.”

Sandhu found a place for himself in the Yang lab. In a few weeks, he plans on focusing more on his own projects.

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).

#IAmScience Sara Ricardez Hernandez

May 7, 2021 By Becca Wolf in #IAmScience Tags: MARC/IMSD, SACNAS, spinal muscular atrophy

By Becca Wolf | Bond LSC

As an undergraduate student, Sara Ricardez Hernandez did not have mentors that exposed her to the many opportunities available for underrepresented students — like summer programs and other research initiatives — but now a graduate student and a Life Sciences fellow, Ricardez Hernandez wants to make sure that no one else is ever in that boat.

“I really like advocating for other people like myself. For example, the university that I went to for undergrad had very little mentoring for minority students, so I want to help people not only be able to get a Ph.D. but be even better scientists and have more opportunities than the ones I had,” said Ricardez Hernandez, a current member of the Chris Lorson lab at Bond Life Sciences Center.

She has not wasted any time. She is currently the vice president of Mizzou’s chapter of the Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS). SACNAS is a program that provides networking and professional development opportunities for minority students.

“We try to help students by hosting workshops and inviting different diverse researchers so students see that they can succeed in academia and become principal investigators too,” Ricardez Hernandez said. “When I first arrived at Mizzou, I knew they had a chapter here and I was very excited about that. I even contacted some people before classes started and I was like, ‘Hey, I’m really interested in becoming a member’ — I had been president for the Hispanic Latino Association in undergrad — so I knew that I wanted to keep helping students.”

Ricardez Hernandez also serves as a graduate student mentor with MARC/IMSD (Maximizing Access to Research Careers/Initiative for Maximizing Student Diversity) at Mizzou. She currently mentors six undergraduate students where she provides support and advice regarding their research, academics, and any personal issues that may be barriers to their success.

“One of my biggest passions is mentoring and trying to push higher education into a more equitable future,” Ricardez Hernandez said. “Historically, higher education has lacked diversity, so we do not see a lot of role models for minority students like professors or PIs. Showing students that, ‘Hey, I’m here at Mizzou, I’m a minority as well and I’m passionate about what I’m doing,’ can demonstrate to undergrads that they can do that too.”

Ricardez Hernandez’s energy is contagious.

“Her mentees think highly of her. She is transparent and vulnerable in sharing her own previous challenges and that makes her so relatable,” Brian Booton, Undergraduate Director of MARC/IMSD at Mizzou, said. “I think we sometimes put mentors on a pedestal and think of them not struggling themselves or that they’ve never had difficulties, but I think she’s really authentic with the ways in which she’s grown. She’s able to reflect on those lessons and reframe them as social capital making her a very effective mentor.”

Ricardez Hernandez extends her passion for education in the lab and her studies as well. She is in the Molecular Pathogenesis and Therapeutics Program where she studies neuromuscular infantile diseases. She is currently working on the characterization of respiratory defects in spinal muscular atrophy with respiratory distress type 1 (SMARD1) and the applications for potential therapeutics.

“I think it keeps me going. Sometimes it’s hard being a graduate student, and not everything works out all the time or you have a lot of things going on but studying diseases like SMARD1 makes me want to come to lab every day and keep doing what I’m doing,” Ricardez Hernandez said.

With a few years left at Mizzou, Ricardez Hernandez plans on helping as many people as she can.

“She’s a real advocate and champion for her mentees,” Booton said. “She’s so approachable and genuine and she’s been a great asset to the program.”

#IAmScience Ellie Swan

April 30, 2021 By Lauren Hines in #IAmScience Tags: Food and natural resources, nutrition

By Lauren Hines | Bond LSC

Whether Ellie Swan is in the gym lifting 200 pounds or in the lab preparing samples, she loves learning how nutrition and exercise affect the body.

“I’ve always really liked exercising and nutrition, and I like learning about that, so it’s interesting to me to learn about it on a very small level on how your body works so that you can have that better understanding,” Swan said. “I feel like once you have that base knowledge, you can take that on a greater scale for your body and use that for exercise and nutrition and not just those basic cellular functions.”

Swan, a sophomore pre-med student, joined the Ruthie Angelovici lab at Bond Life Sciences Center in January and hopes her work there will help her understand nutrition on a molecular level. This semester she maintains the plant growth chamber and helps graduate students with their projects, but Swan plans to work on her own project this summer.

Swan’s love for science started when dealing with medical issues at a young age.

“The type of person that I’ve always been is I want to understand why this is happening so I can fix it,” Swan said. “That kind of generated my love of science because it’s an explanation for everything. Once you have a base knowledge, you can kind of start building on that understanding.”

Exercise and nutrition are a big part of Swan’s life, especially powerlifting. The sport has athletes try to lift a maximal weight in one of the three positions: back squat, bench press and deadlift. Swan currently holds the Missouri state record for the back squat at 285 pounds. She uses the sport to challenge herself.

“I would describe her as somebody who is tenacious, who is extremely caring and sensitive to others, and somebody who is deeply driven goal-driven,” said Ellie Swan’s father Christopher Swan.

Now, Ellie is applying her goals and love of science in the Angelovici lab. Ruthie Angelovici, a principal investigator at Bond LSC, was her former cell biology professor.

“I really really enjoyed her teaching style,” Ellie said. “She’s so knowledgeable. You just could tell in all of her lectures that she just knew what she was talking about. And obviously, I like that she’s a strong female character. That’s something that I can look up to for sure.”

Once Angelovici mentioned she did cell metabolism research in her lab, Ellie realized she wanted to be a part of it.

The lab is currently trying to pinpoint amino acids in seeds so they can fortify these seeds or equip them with all the necessary vitamins and minerals a person needs in a day. By doing so, the lab can bolster food supplies in third-world countries where many people rely on fortified cereals for their vitamins, minerals and proteins.

Now in the lab for about four months, she’s learned that conducting science isn’t what she originally thought it was.

“To learn more about science, you have to be super, super particular and be very, very specific,” Ellie said. “But whenever you find that one it’s like, ‘Ah hah! Here we are. Here we are. We found it.’”

Despite the hurdles, she is known for her positive attitude.

“There’s been plenty of times when she probably had reason to feel down on herself, and maybe did for a little bit, but she was always able to pick herself back up and refocus and get going,” Christopher Swan said. “I think that shows an incredible amount of self-confidence and fortitude.”

A year from now, Ellie plans on taking the MCAT and starting the application process for medical school. She wants to eventually become a dermatologist.

In the meantime, she will be in the Angelovici lab diving into what’s goes on at the molecular level.

Lab explores link between genetic differences and domestication in kale

April 28, 2021 By Becca Wolf in Research Tags: Brassicales, gene expression, kale

Tatiana Arias and Chad Niederhuth studied the plant, kale, in this publication. | “Kale” by photofarmer is licensed under CC BY 2.0

By Becca Wolf | Bond LSC

It is said that variety is the spice of life.

When it comes to kale, much of that variation derives from domestication, and genetic differences that evolved over thousands of years resulted in different color of leaves, nutritional value, and habit and length of growth.

Understanding the links between traits and genes could one day help plant scientists create better vegetables for us.

Eight years ago, Tatiana Arias from the Chris Pires lab and Chad Niederhuth from the John Walker and Paula McSteen lab at Bond Life Sciences Center came together to research leaf differences in this species, Brassica oleracea. Brassica oleracea includes many foods from the vegetable aisle from the grocery store like kale, cabbage, and broccoli.

“In general, people do these types of studies to narrow down some specific genes, but we tried to find a bunch of different genes that could serve different purposes in the future for basic science and developmental biology studies, but also for more applied work in crop sciences,” Arias said.

She and Niederhuth’s broad approach looked at genes that they thought could have been selected during domestication of kale. As humans farmed these leafy greens over millennia, they selected for plants that grew more upright with leaves we liked to eat, developed more ornate foliage and flowered later, differentiating kale from its sisters like broccoli and cauliflower where the flowers were the valued food product.

They compared three morphotypes of Brassica oleracea plants: kale, cabbage, and TO1000 — a specific kale line.

“We brought the evolutionary history of how Kale was domesticated from the other Brassica oleracea morphotypes. Tatiana is really good at the microscope and doing really detailed sections of different parts of the plant as they’re growing,” Chris Pires said. “They sequenced using next gen sequencing, which I’d suppose you’d call it old next gen or postmodern sequencing since it’s been so long.”

While sequencing RNA, the labs found thousands of genes expressed in these different vegetable lines.

“I am a classically trained botanist, so for me it was a very new approach to think about genomics for plants,” Arias said.

While the Pires lab handled the RNA sequencing, Niederhuth in the McSteen lab handled the bioinformatics analysis, the mapping of sequence data, and the identification of the differentially expressed genes.

“It was a team effort between Tatiana and I, she was really the expert in studying these different varieties and their morphological differences and she generated a lot of the data,” Niederhuth said. “I brought to that some of my expertise in gene expression data.”

Through their work, Arias and Niederhuth found 3,958 expressed genes that separated kale from cabbage and TO1000. Some of these differences were in genes that regulate vegetative and reproductive transitions — things that create the very different look of cabbage versus kale.

Some genes they found in kale were particularly interesting. These were involved in leaf morphology, plant structure, and nutrition and were expressed differently, allowing them to identify a set of genes that may be important in kale domestication. Those genes would link, for example, to why kale is more upright and cabbage leaves curl into a head or the variation in color of the leaves.

“I didn’t necessarily know what to expect going into it,” Niederhuth said. “It was interesting to see some results that were related to some of the differences in the phenotypes we observed. Before this I had never worked with Brassica oleracea before, it was the first time I was working with genomic data from a species other than Arabidopsis. It helped me begin working with a variety of different species in many ways.”

While this research was conducted over eight years ago, Arias and Niederhuth recently published the findings.

“It’s nice to have one of many projects off my plate, and I’m glad that it’s finally gotten out there,” Niederhuth said. “This is just how life works where people in this career are oftentimes moving and things get set aside. I am glad that after all these years, we’re finally able to come together again and get it finished.”

To read more of Arias’ and Niederhuth’s research, check out the March article published on the Frontiers in Plant Science website titled, “The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype.”

#IAmScience Katie Horton

April 23, 2021 By Becca Wolf in #IAmScience Tags: botany, plant science

By Becca Wolf | Bond LSC

Katie Horton feels most at home in the shady woods of the Southeastern United States, so much so that she can name and give out a few facts about almost all of the plants.

Horton, a graduate student in the Walter Gassmann lab at Bond Life Sciences Center, moved to Columbia in August, and has a lot to learn about plants native to the Midwest.

“One of the things I’ve struggled with so far is that I don’t know many of the plants here in Columbia by sight. There are some that are pretty widespread and regular, like I recognized most of the weedy-type plants, but we didn’t have Cottonwoods where I am from and that’s one of the biggest trees here,” Horton said. “I can’t wait to get out and hike the trails and look at all of the plants.”

A plant lover through and through, Horton had more than 50 houseplants the last time she counted.

“My boyfriend and I try to make a garden anywhere we go,” Horton said. “We always tell our friends that if they’re doing yard work and if they pay for the plants, they can call us and we’ll do all the planting and design work. We’re in the process of making a garden for food and for flowers at our current rental.”

This energy has been welcomed in the Gassmann lab where she has already taken some undergraduate students under her wing and is planning her own project.

“It’s honestly impressive how much she knows about plants, like the Latin names and the diseases that they might encounter. She can even look at something that she doesn’t know and go through a list of what type of leaves it has, and so on, and make a conclusion,” Sam Smith said.

Smith, an undergraduate student in the Gassmann lab, has become close with Horton in her short time there.

“One time I had finished all of my stuff for the day, and she wanted to show me a flower that bloomed on campus the day before,” Smith said. “So, we left the lab and walked across campus to see it. Once we got to the flower, she was able to tell me its name and a bunch of facts about it. Mizzou is a botanical garden so she’s basically having a field day.”

While Horton is having fun as a graduate student, this all almost did not happen. When she first went to college, she flunked out, and almost flunked out a second time, too.

“There were a lot of ups and downs,” Horton said. “It got to the point where if I failed chemistry one more time, I wouldn’t have been able to be a biology student anymore. I’ve never really seen quitting as an option, though, and as soon as I became interested in botany and plant sciences, that was my only goal. There’s no quitting in life, I can’t just sit down and say ‘okay I’m done,’ I have to keep going. The sun is going to come up again, you can’t just stop.”

Horton credits her previous advisor at the University of North Georgia for keeping her on track.

“The most important thing is finding a mentor or advisor that you really mesh with and is excited about the things that you’re excited about,” Horton said. “If I hadn’t had teachers and professors take an interest in me, I wouldn’t be where I am today.”

In addition to helping in the Gassmann lab, Horton is also a part of the Southern Appalachian Botanical Society (SABS), where she shares her love of plants with others.

SABS has their own science publication and provide scholarships to students and professionals for their botanical research.

“It is a really great way to do outreach for students and to get young people involved in botany,” Horton said. “I want to help rejuvenate the membership needs and get people excited about native ecosystemms and the way that things interact with each other.”

Even though she does not live in the Southeastern United States anymore, Horton is able to stay connected to the program online.

“We mostly meet online because we’re from all over the southeast,” Horton said. “I am able to meet all these botanists from the whole southeast and we share pictures with each other, and I think it’s great, the sense of community that it builds, and the outreach that you get, being part of something that is so wide.”

In the meantime, Horton is preparing for her first committee meeting for her graduate project here at Bond LSC, and plans on going on many hikes this summer.

“I’ve got plans out to go hiking with friends already,” Horton said. “We’ve got plant people, bird people, insect people…It’s going to be a lot of fun.”

Diller Costello Awarded Highly Competitive NIH Fellowship

April 21, 2021 By Lauren Hines in Research Tags: NHBLI, NIH, skeletal muscle regeneration

By Lauren Hines | Bond LSC

Alexandra Diller Costello, a biology graduate student in the D Cornelison lab in Bond Life Sciences Center, recently received a three-year NIH fellowship from the National Heart, Blood and Lung Institute.

It provides Diller Costello with funding to pursue her work on muscle and blood vessel regeneration for three years.

The fellowship comes as a result of her proposal titled, “Signaling in the Microvasculature During Skeletal Muscle Regeneration.” Diller Costello’s research focuses on the coordination between muscles and blood vessels during muscle regeneration in adult mice. Diller Costello is also developing a novel method of 3D co-culture using primary muscle and endothelial cells to expand her investigation.

The study is part of a collaboration between the Cornelison lab at the Bond LSC and the Segal lab in the Medical Pharmacology and Physiology department at the MU School of Medicine.

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