Research

Bringing Protection Back in Line

July 23, 2021 By Suppes, Davis (MU-Student) in Research Tags: Mizzou Research

Research refines platform to address immune disorders

Dr. Esma Yolcu and Dr. Haval Shirwan, Co-pioneers of ProtEx technology

By Davis Suppes | Bond LSC

The things that protect you can also cause the most harm. That’s especially true when it comes to your immune system, which protects you against infections, but is also responsible for a host of diseases, including autoimmune disorders, such as type 1 diabetes.

More than 1.4 million Americans suffer from the self-harming condition of diabetes without an effective cure, but researchers Haval Shirwan and Esma Yolcu may have the answer.

The pair tackle the problem of diabetes and other autoimmune disorders by targeting the component of the immune system that does harm for modulation. DNA-based gene therapy has traditionally been used as a scheme to modulate the immune system.

“DNA-based gene therapy is a complicated, exhaustive and expensive technology,” said Shirwan, a NextGen Precision Health researcher at the University of Missouri and a professor in the Department of Child Health and Molecular Microbiology and Immunology at the School of Medicine. “We wanted to see if there was a more efficient and practical way to do immunomodulation.”

For conditions like Type 1 diabetes, where the immune system misfires and destroy beta cells producing insulin, they target to replace defective islets with healthy ones from another individual. Insulin is an important hormone that plays a role in regulating your blood sugar level. A major hurdle for islet transplantation is the immune rejection.

Shirwan and Yolcu co-pioneered ProtEx™, a proprietary platform that allows for generation of novel recombinant immune ligands and their positional display as single agents or in combination on biological surfaces, such as islets. This is a practical and safe alternative to gene therapy for localized immunomodulation.

In traditional methods of gene therapy, DNA must first be introduced into the cell, but ProtEx technology bypasses that step. Sticking the protein directly on the cell surface for immunotherapy via a test tube allows for a safer, more effective method than gene therapy. Islets engineered to stick on their surface proteins evade rejection by the immune system.

Shirwan’s translational research program’s goal is to develop safe and practical immunomodulatory approaches with applications to transplantation, autoimmunity, cancer, and infections. On the cancer side, Shirwan and Yolcu team has shown that the immune system of a healthy individual can be trained to surveillance the body for cells that may transform into cancer and eliminate them before cancer takes hold. “This is an exciting finding that has not been reported in the literature and sets the stage for

Shirwan’s focus of learning about the immune system and improving it came to him very early when he was a virologist for University of California, Santa Barbara. He developed an interest in immunology and wanted to learn more about immune defense mechanisms. Before bringing his talents to Mizzou he also spent time working at the California Institute of Technology, Allegheny University of the Health Sciences, University of Louisville, and Cedars-Sinai Medical Center.

He believes preventing these cancers and infections is the route we should be aiming toward, rather than trying to find new ways to treat them after they have already damaged the body to an extent.

“Things like cancer are so effective and harmful because they use the same mechanism as the immune system to evade it,” Dr. Shirwan said, “Just like how a runner can build muscle memory for running, our immune system can learn and build up a memory of these pathogens and infections to create a more effective response.”

“This is just the tip of the iceberg,” Dr. Shirwan said, “I am very excited to continue expanding on what our immune system is capable of.”

This type of research contributes to the University of Missouri System’s NextGen Precision Health focus. The NextGen Initiative unites scientists, government and industry leaders with innovators from across the system’s four research universities in pursuit of life-changing precision health advancements.

Dr. Shirwan and his team are moving to the new NextGen building on Mizzou’s campus in mid-September. He is very thankful for getting the opportunity to work in these facilities with these people, and he is excited for the next step of their research.

Shirwan believes we have only scratched the surface of what our immune system is capable of. Our immune system may not always know what is good and bad for itself but one thing is for sure, Dr. Haval Shirwan is good for it.

How a pandemic spreads

July 16, 2021 By Roger Meissen in Research Tags: COVID-19

COVID-19 analysis looks at variant spread

Saathvik Kannan, Kamal Signh, and Austin Spratt — Saathvik Kannan, Kamal Singh, and Austin Spratt, worked together at Bond LSC to identify new SARS-CoV-2 variants. | photo by Davis Suppes, Bond LSC

By Davis Suppes | Bond LSC

Variants of the virus that causes COVID-19 continue to plague the world with spikes in infection, keeping the current pandemic from being fully controlled as Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections remain unmanageable in some parts of the world.

Researchers at Bond Life Sciences Center and the University of Nebraska Medical Center (UNMC) have been conducting research on mutations in four new variants, B.1.1.7, B.1.351, P.1 and CAL.20C. These evolving variants appear to be more infectious and transmissible than the original Wuhan-Hu-1 virus.

It all started with a new spike in infections of a variant of SARS-CoV-2 in the UK. Despite a slowdown in infections due to precautions of masks and lockdowns, the new spike meant something about the virus had changed.

“Our goal was to find out where these variants are distributed, and how they are migrating,” said Kamal Singh, Assistant Director Molecular Interactions Core, and scientist at Bond LSC. Singh was a corresponding author on the paper and has been at Bond LSC for 12 years.

Their work showed completely different mutations in these variants based on regions, but also where variants have common lineage. That commonality can be seen between the CAL.20C and B.1.351 variants.

While related to each other, they also developed different mutations.

“B.1.1.7 was more infectious and was able to spread to more people. It slowly dominated and that’s what happened in the United States as B.1.1.7 is now the dominant variant of SARS-CoV-2 in the US,” said Saathvik Kannan, a co-author. Kannan is going to be a 10th grader at Columbia’s Hickman High School this fall but works under Singh at Bond LSC as a computer programmer and researcher.

Once they identified the related COVID-19 variants, they wanted to trace their migration. This allows them to see where the mutations are being carried and which regions have a more dense number of infections. The prevalence of variants was key in identifying where they were moving.

Their analysis looked at certain mutations in each variant to see how they were related, why some sequences have mutations that others don’t and tried to determine how they evolved from their original sequence.

By comparing the structure of each virus, they were able to illustrate how the related mutations moved state by state across the country.

Sankey diagram variant CAL.20C US.jpg — This Sankey diagram for variant CAL.20C in the United States.They aligned the first-known CAL.20C sequences from each state then grouped the sequences based upon the date collected and closely their structures matched, with cut-offs of 96, 94, 93, 92, 91 and 90 percent compared with the previous group.

“It is pretty clear that some states have a higher homology match, which helps us see a pretty linear trend of migration from the Western states to the East in the United States,” said Austin Spratt, a computer science senior and lead author on the paper. Spratt has worked under Singh at Bond LSC for two years.

The study cautions that the sequences of viruses are being deposited at an unprecedented rate, so it is possible that some conclusions may change as more sequences of variants become available.

“These variants are continuously evolving and complex in nature, but a proper understanding of what makes each variant unique, its genetic makeup and its interaction with host proteins is critical to developing the most effective vaccine,” said co-corresponding author Siddappa Byrareddy, Professor & Vice-Chair of Research, in the Department of Pharmacology & Experimental Neuroscience, at the University of Nebraska Medical Center. “Not only will this help us to design better vaccines now, but greatly help us to be prepared to deal with more mutant variants in the future.”

Although analysis indicates that mutations only in one variant do not reflect evolution of it, these genetic mistakes may increase infectiousness of a particular variant

The short period of time, volume of variants and limited travel around the world all point to a greater infectivity than the original (Wuhan-Hu-1) virus. Recent deadly surges in India caused by variant B.1.617.2 or the Delta variant will soon be added to their analysis to further understand the COVID-19 pandemic.

Their research was published in the paper ‘Evolution, Correlation, Structural Impact and Dynamics of Emerging SARS-CoV-2 Variants’ in the “Computational and Structural Biotechnology Journal” on June 19, 2021.
Funding provided by: Bond LSC, Swedish research Council, American Lung Association, National Institute of Dental and Craniofacial Research in collaboration with Prof. Gary Weisman of the Bond Life Sciences center.

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.

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).

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.”

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.

Trying to understand amino acid regulation for the good of humanity

April 14, 2021 By Becca Wolf in Research Tags: amino acids, nutrition

Abou Yobi working in the Ruthie Angelovici lab. | photo by Becca Wolf, Bond LSC

By Becca Wolf | Bond LSC

Many works aimed at improving seed nutritional quality have been faced with limited success because of the lack of clear understanding of how amino acids are regulated. Abou Yobi wanted to get to the bottom of this.

Yobi, lab supervisor in the Ruthie Angelovici lab at Bond Life Sciences Center, has been working on understanding how amino acids are regulated in seeds for years.

“We can use that understanding to improve seed quality in crop plants so can we increase those essential amino acids,” Yobi said. “Developing countries rely heavily on crops like wheat and maize, but they need to find a crop that could provide them with those amino acids.”

Essential amino acids are a vital part of nutrition that cannot be made by our body, so we have to get them from food like soybeans, quinoa, and eggs.

“We know that most crops lack at least one or two of these essential amino acids,” Yobi said. “For many years, scientists have been trying to improve those amino acids, but the outcome was always minor because of how seeds regulate their protein-bound amino acids to maintain a specific composition. Until we fully understand of such regulation, any effort aimed at improving seed quality through increasing the composition of essential amino acids would be unsuccessful.”

To do this, Yobi uses multi-omics approaches and bioinformatics tools to identify amino acid differences that occurred through natural variation and associate them with proteins and genes. This approach combined with using a large set of seed storage protein mutants could help identify targets for seed biofortification.

Clement Bagaza, a graduate student in the Angelovici lab, works with Yobi in trying to understand how they can alter the seed and grain amino acids for the benefit of nutritional value to humans and animals.

“I grow 1,001 and 360 Arabidopsis ecotypes populations twice, these populations in combination with maize populations are being used in the lab to try and come up with genes that are involved in amino acids metabolism. These are huge populations to deal with,” Bagaza said.

That is a lot to handle, so they collaborate with other labs to balance out the workload. Collaborators look to the Angelovici lab’s vast knowledge of amino acids and their amino acid analysis for help with their own research.

“Different scientists on campus and off are interested to incorporate the analysis of amino acids in their research, and this opened a lot of collaborations with Angelovici’s lab which provides that service,” Bagaza said. “We’re the lab you should look at if you want to do some amino acid analysis.”

For Yobi, seeing the lab gain more collaborations and recognition has been exciting.

“A lot of people, not just from our university here, but from other universities, are coming and collaborating with us on this and it’s very rewarding to know that what you’re doing is very interesting to other people, not just to you personally,” Yobi said.

Yobi and Bagaza hope that these collaborations lead to more discoveries on how to regulate essential amino acids to improve crops.

“I am from a place [Rwanda] where nutrition is a problem,” Bagaza said. “Not only my place where people can face both malnutrition and undernutrition, but other places of the world might face one or both of these issues. Having enough on the table doesn’t mean you’re eating heatlhy, we should also think about the content of what we are eating.”

While they have worked on this research for years, Yobi and Bagaza are confident they will continue to find answers to improve the nutrition of others.

“We have a lot of publications, we have a good number of collaborators, and things are moving very well so far,” Yobi said. “We are looking forward to being able to do good things for the good of humanity.”

Defense or growth: a complicated balance

April 7, 2021 By Lauren Hines in Research Tags: gene expression, plant immune system, plant science, TOPLESS gene family

By Lauren Hines | Bond LSC

The plant immune system isn’t active all the time. Plants must decide to either defend against disease or grow, but not simultaneously.

The reason behind this process is not fully understood, and the Walter Gassmann lab at Bond Life Sciences Center is searching for answers.

The lab recently found a link between members of the TOPLESS gene family, the immune receptor SNC1 and a negative regulator SRFR1. The relationship revealed when members of the gene family are absent in a plant, the immune system intensifies, and growth is stunted. The findings were published in February in the journal PLoS Genetics.

“As scientists, we try to simplify a model but sometimes the more we know, the more complicated we realize it to be,” said Jianbin Su, a research scientist in the Gassmann lab.

The study focused on TPR2 and TPR3, two genes within the TOPLESS family.

After studying these two genes, Gassmann said they did not act as he expected when partnered with SNC1. It turns out the genes act as “brakes” so then the immune system doesn’t go on forever.

“If you were to keep stimulating a plant with pathogens, you would see reduced growth over the long term,” said Gassmann, director of Bond LSC. “Plants have to balance whether they grow or if they defend, but we can artificially remove genes in the repertoire of a plant so that the immune system is on all the time from the get-go, and that manifests itself as stunted growth.”

This balance is the main obstacle facing researchers who want to increase crop yield and resistance to disease. Technically, researchers could increase the level of resistance in plants today but increasing the defense system often costs too much growth and yield.

Instead, the Gassmann lab proposes to modify the natural regulation of the plant’s immune system and bypass artificially increased resistance like pesticides.

“In the end, we would like to be able to generate crop plants that are more resistant to a wide swath of pathogens once we understand their regulatory system better,” Gassmann said.

Now, all the Gassmann lab needs to do is figure out how the system works. Easier said than done.

However, there are theories as to why the plant must choose between growth and defense. Previous theories believe there isn’t enough energy for plants to defend and grow at the same time. Gassmann said the theory doesn’t make a lot of sense to him. Even though the plants at Bond LSC are “pampered” and live in a “luxurious environment,” they stop growing whenever their immune systems are stimulated.

“I think evolutionarily, it is an advantage for plants to have a genetic circuit that makes them decide whether to grow or to defend themselves,” Gassmann said. “So, it’s not an energy limitation. It is genetic pathways that we can study to understand how that recognition works. And if there’s a genetic circuit, then we can tweak it and improve on it.”

Even with these theories, there’s more to this system than just genetics. While TPR2 and TPR3 interact with the immune receptor SNC1 and a negative regulator SRFR1 — a molecule that puts a stop or pause on a cellular process — that doesn’t mean their proteins interact in the cell.

“In terms of protein-protein interaction, many people think, ‘Oh it’s just as we interact physically,’ but actually, the cell is alive,” Su said. “In microscopes, they are moving. Sometimes the protein interaction needs a trigger to induce the protein-protein interaction.”

This interaction at the protein level still needs to be further analyzed, but it can explain why both SRFR1 and TPR2 must be absent for the plant to stop growing and be smaller.

“We think they actually work at different points in the circuit, and that’s why you get an additive effect on plant growth,” Gassmann said. “We’d be really interested to find out what those points are exactly, so there’s always more work to be done.”

While the Gassmann lab has found a new interaction revealing a bit more of the plant immunity process, there is still more to understand.

“Knocking out SRFR1 causes smaller plants, but the more accurate mechanism is still, I think, largely unknown,” Su said. “These genetic interactions with TPR2 are just one part of SRFR1 as a negative regulator in plant immunity.”

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