2021 June

June 2021

#IAmScience Lyndon Coghill

June 24, 2021 By Suppes, Davis (MU-Student) in #IAmScience Tags: bioinformatics, Mizzou Research

Lyndon Coghill is the new Director of the Bioinformatics and Analytics Core, and he is already making big moves at Mizzou.

By Davis Suppes | Bond LSC

Lyndon Coghill’s official title may be Director of Informatics for the Bioinformatics and Analytics Core, but his job branches out much wider than just a single label. Even as an undergrad, Coghill wore many different hats.

“I was incredibly excited about the way that the MU Office of Research and Economic Development recruited me,” Coghill said, “With these types of processes you can get an idea as to whether or not an institution is actually committed and excited about building something out.”

With his experience and range of expertise, Coghill was an easy choice for Mizzou to fill the role of Director of the Bioinformatics and Analytics Core located at Bond Life Sciences Center.

Before he achieved his doctorate in biology, he completed his undergraduate degree in zoology with minors in microbiology and geology at Western Illinois University. For his dissertation, the research he conducted was focused heavily on evolutionary genomics. Simply put, he wanted to know how changes in the genome lead to changes in a physical organism that allow them to adapt better to different environments and conditions.

With his doctorate in biology, he would go on to his first postdoc at The Field Museum of Natural History in Chicago in 2013, and then on to Louisiana State University where he began his role as a senior post doctorate in 2015. He continued to diversify his portfolio there working with the department of biology, focusing on computational biology. He was then promoted to research data scientist which had him take on an even more computationally heavy role. With this, he was able to help biologists learn how to talk to computer scientists, and assist them with building collaborative programs together..

As director, Coghill’s mission is to provide bioinformatics and data science support to all researchers across the UM system. He is creating a central hub where faculty who want to conduct domain- specific biological or life sciences-related research that is computationally heavy can get the help they need to come up with solutions. He does this by helping researchers wrangle incredibly large datasets and by helping them understand what that data is telling them from an information perspective in a meaningful way.

Coghill mentioned how interim Vice Chancellor of Research and Economic Development Thomas Spencer also made a personal effort to make sure Coghill understood his vision going forward on campus “and for me that was enough of a selling point that I wanted to be a part of that,” Coghill said.

In addition to the thorough recruitment process, Mizzou’s facilities and access were other huge factors that Coghill was looking forward to once he got here. With a hospital, vet school and productive biology program all on the same campus instead of in different cities, Mizzou offers a unique opportunity to build the integrated program all in one place.

“We’re trying to reach out to every department on campus to build these relationships because you can’t have true integration of ideas and solutions if you don’t talk to everyone who might be a benefactor or have knowledge about that,” Coghill said.

Coghill believes that to create a phenomenal translational research program, this core must interact with all these programs so that experts of different fields can come together to collaborate.

“Informatics research, especially bioinformatics is a program that really forces you to keep one foot in both worlds of computer science and biology, and there’s a limited number of people who do that kind of work,” Coghill said, “I think that was one of the big pushes for getting my experience here for this position, to bring in somebody who could bring these programs together and integrate across all these different fields.”

Coghill is excited to be working with the variety of researchers and programs across the MU campus and UM System, and learning from them at the same time.

“We may not know their biological system as well as they do and we may not know the high performance computing system as well as a full-time systems administrator, but we know enough of both that we can communicate with both teams and make sure that we can help get the researchers from the starting point to a meaningful result,” Coghill said.

Their goal is to provide Mizzou and sister campuses with research support allowing faculty to build translational research programs using computing power and informatics. This core brings new opportunities for Mizzou students as well.

“We’re going to have programs for students that can rotate through as part of the Informatics and Data Science Institute,” Coghill said.

This means that students who are interested in research fields can get direct experience related to career possibilities outside of Mizzou and academics by working in this program.

“Students can come to us and learn basic coding skills, learn informatics and bioinformatics, and that will help them build a skillset that will make them quite employable,” Coghill said.

Between helping researchers in their labs and analyzing quantities of data they are gathering for the first time, Coghill has a variety of jobs he has to understand and execute.

“So, I am the guy who wears a lot of different hats and allows these researchers from different domains to talk to each other,” Coghill said. “We’re trying to help them get to the point where their work could be as big as they want.”

Mizzou and Coghill know that there is no way to push modern research without computing, especially at the scale research is done today.

It would be extremely rare for someone who has a doctorate and spent their life trying to understand how one particular part of a biological process works to also have a doctorate in computer science, “That’s where we help… we’re providing researchers with the tools to do research at a scale using computing power, and asking questions that for many, might have only been dreamed about at other times in their careers,” Coghill said.

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.”