RNA

Unknown Origins

November 9, 2020 By Lauren Hines in Research Tags: NASA, RNA

$5 million grant awarded to study RNA’s place in start of life on Earth

In his lab at Bond LSC, Donald Burke-Agüero examines his model of the RNA protein structure. | Photo by Lauren Hines, Bond LSC

By Lauren Hines | Bond LSC

The search for life on other planets may seem quite literally out of reach, but the search actually starts here, on Earth.

“Something that guides people in thinking about how life might come about on other worlds is trying to understand how life might have started here on this planet,” said Donald Burke-Agüero, principal investigator at Bond Life Sciences Center and professor of Molecular Microbiology & Immunology in the MU School of Medicine.

The Burke lab recently won a $5 million Interdisciplinary Consortium for Astrobiology Research (ICAR) award from NASA in partnership with eight other institutions. The award will fund their proposal to study RNA as a model for the origins of life.

Scientists hypothesize that RNA, a nucleic acid, was at the heart of molecular processes when life started around 4 billion years ago. RNA is like DNA in that it is a set of instructions and can store genetic information about basic building blocks for life, but it can also perform chemical reactions like enzymes. These two functions help speed up reactions to make important molecules needed for life.

“Becoming part of this has been over 20 years in the making for me,” Burke said. “It’s a theme that I care about tremendously, which is providing a really solid experimental foundation for some of the speculation about how life may have started.”

Burke found out about the grant while he was in another zoom meeting.

“I went back to the meeting and said, ‘Guys, I can’t stay. I’m not paying attention to anything you’re saying right now. Have fun. I’m bouncing off the walls,’” Burke said.

The predecessor to the ICAR program was the NASA Astrobiology Institute, which first called for members in 1998. Burke was starting his first faculty position back then. He always wanted to be a part of it, but it never quite worked out until now.

The “RNA World Hypothesis” has intrigued and driven scientists since the 1960s but has been increasingly explored in the past three decades as technological advances have allowed scientists to look for evidence to support it.

“Part of being in the origin of life team is working with RNA and to expand its known limitations,” said Jordyn Lucas, a Ph.D. student in the Burke lab. “We also like to explore how various modifications could make RNA better at doing a specific job, or how can it make it more durable under certain conditions.”

While RNA can make some reactions, it is possible that a certain set of modifications, tools or conditions could push RNA to perform more like an enzyme. This grant will help the Burke lab find those conditions if there are any.

“It’s kind of like a tool,” Lucas said. “It’s like if I gave you a piece of paper, asked you to write an essay, but I didn’t give you a pen. You can’t do it. It’s not because you don’t have the ability to do it. You just don’t have the right tools.”

Those tools can be hard even for humans to access.

A tube the size of your fingertip can contain quadrillions of RNA molecules and therefore quadrillions of sequences. That’s not an exaggeration. You can imagine how difficult it would be to sift through all that by testing them one by one. It wasn’t until in vitro evolution — a method that screens through large amounts of nucleic acid sequences — in the 1990s that scientists could explore many questions about RNA. Even with that, today’s technology is limited.

“Part of what this grant is going to do is attack that problem to try to specifically do the things that have been technologically very difficult,” Burke said.

The aim of the proposal is to push the limits of what RNA is capable of doing. These findings could bring the RNA World theory closer to being an established fact. This would help NASA know what conditions to look for life on other planets.

The technological advances from this project will also have implications for synthetic biology applications like biomedicines and biofuels. The goal is to find ways in which parts of modern biology can be replaced with RNA that can do something similar.

“Obviously, understanding our place in the universe and how we came about is a big deal and would be a societal benefit, but also a tangible thing that helps somebody be healthier,” Burke said. “That’s important too.”

Further exploring RNA brings us one step closer to a model of the origins of life on Earth and even life on other planets.

“We have no idea how likely life is,” Burke said. “If we can help demonstrate some of the ways that life comes into existence, it will really help to understand how many neighbors we might have on other worlds. And whether we’re likely to have any neighbors at all.”

Institutions involved in the proposal are the University of Missouri in Columbia, St. Louis University, Purdue University, University of Southern Mississippi, University of California in Irvine, University of California in San Diego, University of Washington in Seattle and University of California in Los Angeles.

NASA Selects New Science Teams for Astrobiology Research

Using improved technology to create an Immune Cell Atlas

October 28, 2020 By Becca Wolf in Research Tags: agriculture, gene expression, RNA

Ashley Meyer | photo by Mariah Cox, Bond LSC

By Becca Wolf | Bond LSC

When given an opportunity to use the newest technology, one has to take it.

Ashley Meyer, the lab supervisor of the Wes Warren lab at Bond Life Sciences Center, recently started using the improved technology of single cell RNA sequencing to create an Immune Cell Atlas for chickens. This search browser of sorts allows people to search for cells and gene expression in chickens.

“It would be a platform for researchers to have a baseline of what should be normal, and then be able to run comparative experiments to say ‘Okay, if we challenge this chicken with this disease, what biological response are we seeing?’ Which can help you then understand the disease better,” Meyer said. “Like, ‘How is it being transmitted? How is this chicken reacting to it?’”

Poultry is one of the largest agricultural industries in Missouri, so it is important to keep chickens healthy.

“The Immune Cell Atlas will help us analyze tissues and will help us perform the single cell RNA sequencing on them to ask what’s normal and what’s diseased so that we can see what’s happening,” Meyer said. “It will also allow us to see which chickens are more susceptible than others or how the progression diseases happen.”

Meyer and the Warren lab are some of the first researchers to apply this technology to chicken based research.

Single cell RNA sequencing (RNAseq) allows Meyer to sequence the RNA of an individual cell which provides in-depth data. This can be done using single cell RNAseq which uses the entire cell, or it can be done using single nuclei RNAseq which uses just the nucleus of a cell. This profiles gene expression in cells that make up a tissue to get data on a cellular level to understand the composition of cells.

It is important to target the RNA because it is the messenger that brings instructions from the DNA for controlling the synthesis of proteins. RNA is commonly synthesized in the nucleus of a cell.

“We’re some of the first people to get our hands on some avian single cell data, specifically looking at nuclei. My job is a lot of optimizing these protocols to isolate these nuclei,” Meyer said.

Using nuclei allows Meyer to use samples that have been frozen, collected in other locations, etc., which provides more flexibility.

Isolating the nuclei through RNAseq allows Meyer to identify different cell types based on genes being expressed in a cell in an organ such as a spleen or lung. This information can then be added to the Immune Cell Atlas.

Meyer is a part of a team working on this project including two master’s students, a bioinformatics analyst, and principal investigator, Wes Warren, at Bond LSC, as well as a bioinformatics analyst who works remotely from Santa Cruz, California.

While the team is working from around the country, they are all connected by a common goal.

“Things have been pretty hectic, the break with the COVID quarantine kind of paused everything and then when we got back it just kind of took off, we’ve generated a couple data sets just in the last month or so,” Meyer said.

Having started this research about six months ago, they still have a way to go. Meyer and her collaborators are currently focused on analyzing five to six immune system organs, and plan on expanding in the future.

Since single cell RNAseq is so new, it can be challenging being one of the first labs to use it at MU and in the avian community.

“Since it’s still newer, everyone’s still figuring out how it works,” Meyer said. “Everybody’s determining their own way of analyzing the data. We’re working through the hiccups of everything, and not having years and years of research to guide us can be challenging; however, also exciting because then we can find what works and what doesn’t work which is the whole point of science.”

While challenging, it is rewarding. Meyer hopes that in the future once they have created the chicken Immune Cell Atlas, they are able to expand to other animals.

“It’s exciting to be part of something that’s newer and having something that could be beneficial for other researchers,” Meyer said. “I am a huge advocate for sharing science and teaching science so creating something to aid other research is super empowering for me.”

A Big Load: Using Wastewater to Test For COVID-19

September 11, 2020 By Becca Wolf in Research Tags: COVID-19, RNA

Marc Johnson collecting pellets in his lab. | photo by Becca Wolf, Bond LSC

By Becca Wolf | Bond LSC

There is not much thought that goes into using the bathroom. You do your business, flush, and wash your hands. It is just a part of the daily routine.

Recently though, human waste has become a golden nugget to researchers. In fact, waste from toilets throughout the community are contributing to figuring out where the next COVID-19 outbreak could happen.

And Marc Johnson, Bond Life Sciences Center principal investigator and MU professor of molecular microbiology and immunology, is the person figuring out how this human waste can be an asset as he processes samples from the sewer systems of more than 70 communities across the state.

A map of the sewersheds Marc Johnson’s lab receives samples from. | map contributed by Marc Johnson

These samples may be able to serve as the canary in the coal mine before large outbreaks strike in a community, allowing health officials to prepare for and potentially prevent the spread of COVID-19.

SARS-CoV-2, the virus that causes COVID-19, appears in wastewater several days before an infected person shows symptoms, so Johnson wants to find a faster way to test for the virus.

“We’re very good at predicting what’s happening right now based on samples we collected five days ago,” Johnson said, “We are predicting the future, we just don’t know what our prediction is until the future is actually here.”

This data may not seem helpful, however, it proves that the COVID-19 case numbers are accurate and, if acted upon quickly, can prevent an outbreak in a concentrated population such as prisons or schools.

“With the students, when you’re talking about patients that don’t necessarily know they’re infected, it can be really helpful to have a heads up that this dorm has some infections even if they don’t know it,” he said.

Testing wastewater for SARS-CoV-2—an RNA virus—consists of two phases. Phase one is obtaining the sample and phase two is RNA extraction.

Starting phase one, Johnson receives a 24 hour composite from a wastewater testing facility, “So that no matter when, it doesn’t matter whenever people go, as long as they go once a day we’ll catch them,” he said. This gives his lab a representative sample of the population.

Once the sample is taken from a wastewater treatment facility, it is put into a courier system that brings it to the state lab in Jefferson City, Mo. After it arrives there, the Missouri Department of Natural Resources brings them to Johnson’s lab at Bond LSC so he can begin phase two, RNA extraction.

In Johnson’s lab, the samples are put through a filter that nothing bigger than a virus can get through. This eliminates the solids and other bacteria in the wastewater. Next, a chemical is added that allows the viral particles to stick together so they can be pelleted.

This is then put in a centrifuge and is spun for a few hours to get a small, invisible pellet. RNA is then extracted from this pellet in a QIAcube, a robot Johnson’s lab purchased for this project. The QIAcube is the same robot used by the Missouri Department of Health Services for COVID-19 testing in their own facilities.

Marc Johnson placing the samples in the QIAcube. | photo by Becca Wolf, Bond LSC

After Johnson extracts the RNA, the samples are sent to Chung-ho Lin, MU research associate professor at the College of Agriculture, Food and Natural Resources, who continues testing.

This whole process takes about five days.

Johnson hopes that test results will soon go public so people have an idea of where outbreaks are, although reading the data can be confusing.

Said Johnson, “I think we all agree we’ll be better if we put the data out the way we want it to be seen, because it’s just when you look at the raw numbers, without understanding how to interpret it, you can make any conclusion you want.”

It will be a learning curve for the public to be able to understand the data. Johnson even struggled with it at first, “We learned this lesson the hard way,” he said, “I freaked out several times where I thought I had just discovered Armageddon going to our state, but you have to put it in perspective. When you figure out how much it actually takes to get a signal and how big the sewer shed sample is, it’s like, ‘No okay, that’s normal.’”

Along with other testing sites, Johnson’s lab has been testing several universities and colleges in the state, including MU. With time and improvements, it is realistic that his lab will be able to predict the number of infected patients in an area.

“It’s a crap ton of work,” Johnson said, “But it’s kind of interesting. It worked far better than I would have expected.”

While research on COVID-19 was not on Johnson’s agenda earlier this year, he has been trying to have fun with it.

“The puns are unending,” he said, “There are just so many great puns I’ve gotten out of it.”

“It’s serious research but it’s nice that the topic has gotten a little bit of levity.”

#IAmScience Madeline McFarland

December 8, 2017 By Allison Scott in #IAmScience Tags: biochemistry, RNA

Madeline McFarland, a senior biochemistry major, works in the Burke Lab in Bond LSC. | photo by Allison Scott, Bond LSC

By Allison Scott | Bond Life Sciences Center

“#IAmScience because research has really shaped the way I think about things.”

Science isn’t limited to the lab. It’s more of a mindset than a discipline, and Madeline McFarland knows this all too well.

As a senior biochemistry major working in Donald Burke’s lab in Bond LSC, McFarland experiments with ribonucleic acid (RNA) to study the origin of life before DNA and protein served as genetic material and catalyst, respectively.

“I’m interested in the RNA World Hypothesis and how RNA may have played a role in getting life started on our planet,” McFarland said.

This hypothesis suggests early forms of life on Earth may have relied solely on RNA to store genetic information and to catalalyze, or spur, chemical reactions. The theory goes that DNA eventually evolved to take its place due to the instability and ineffectiveness of RNA.

In the lab, McFarland focuses on using a program called systematic evolution of ligands by exponential enrichment (SELEX), which filters the RNA so she can find which strands do what she’s looking for. Specifically, she’s trying to determine if the RNA can make a reaction happen. If McFarland can find this connection, scientists would see that as support for for the RNA World Hypothesis.

“I’m trying to see which RNAs can perform a catalytic function,” McFarland said. “By doing that, we can kind of start to think about how RNA used to function in early earth.”

Her typical day starts at 9 a.m. when she heads to Bond LSC to get her experiments set up for the day.

“I go to class while they’re incubating,” McFarland said. “My science allows me to set stuff up and have a break while it’s running. I’m usually running experiments four days a week.”

McFarland was inspired by the work being done in Bond LSC and the analytical way of thinking about experiments.

“[Research] is kind of nailed into you as soon as you step on campus,” McFarland said. “That was the motivating factor, but I came to love it for a lot of reasons. It’s really shaped the way I think about things.”

When she’s not wearing her lab coat and investigating the origins of life, McFarland spends her time working in environmental efforts at Mizzou.

“I’m really passionate about sustainability in all of its forms: environmental, economic and social,” McFarland said. “I lead the electronic waste drives around campus, and I’m co-directing sustainability week this year.”

McFarland is also a co-president of the biochemistry club.

“In our meetings, we bring in grad students and faculty to talk about career options, so everyone can ask questions,” McFarland said. “We also do fun events. Last night, we had a biochemistry-themed breakout room. They had to balance chemical equations and transcribe and translate a DNA sequence to spell out a word. We have a lot of fun with it.”

All of her work in the lab in combination with her research at Bond LSC has only strengthened her bid for her next endeavor: medical school.

“I’m passionate about communicating science, and I think medicine would allow me to do that,” McFarland said. “I like the idea of radiology because it allows you to look at an image, or data, then think through things on your own, which is a lot like research.”

If she doesn’t end up at medical school, McFarland would like to continue to pursue education. She could see herself attending graduate school.

“I’m interested in a master’s in public health,” McFarland said. “It would allow me to expand my knowledge of science and how it relates to health beyond the scope of the lab.”

Regardless of if she continues to learn through medical or graduate school, though, McFarland credits research for having an immense impact on her career.

“Research has really shaped the way I think about things,” McFarland said.

Dr. Burke wins Distinguished Professor Award

November 14, 2017 By Samantha Kummerer in Research Tags: DNA, RNA

By Samantha Kummerer | Bond LSC

“He’s a triple threat in science,” Bond Life Sciences researcher David Pintel said.

Donald Burke’s combination of scientific excellence, caring mentorship and devotion to the University of Missouri led Pintel to nominate Burke for the 2017 William H. Byler Distinguished Professor Award.

The university agreed, awarding him the honor in October.

The University-wide accolade recognizes a faculty member for their “outstanding abilities, performance, and character.” When Pintel read this description he said he instantly thought of Burke.

This is the first time a faculty member from Bond LSC has won the award. Pintel said the award shows the quality of people here and the department is proud of him for receiving it.

Burke is a Molecular Microbiology & Immunology professor. His lab in Bond LSC studies RNA, the molecule used to help cells copy genetic information from DNA.

For Burke, the award is an honor.

“You always try to do everything you can to contribute to making the place great and you don’t do it for the purpose of being recognized, yet when the recognition happens, it’s nice,” he said.

Burke’s lab hosts students from the high-school to post-doctoral level. For each member, Burke said he tries to figure out their motivation. He starts by just asking questions and is able to align their goals and his.

“You can’t just say ‘This is what we do in my lab, deal with it.’ You can’t do that,” Burke elaborated, “Yes, it’s a lot of work and a lot of effort, but it has ceased being a burden for me. Now, I think of it as a new fun challenge.”

He said that challenge has paid off because every student that has gone through his lab has taken his science in new directions.

Pintel said this connection Burke has with his students is easy to see.

“People in his lab love him and, to me, that’s always a good sign,” Pintel said. “When I see people in a lab like that, I know it’s a good environment. That always means something good is going on.”

During their time in his lab, Burke tries to teach his students the importance of working as a team as well as learning understand the research process.

“Some of the things I’m most proud of aren’t necessarily the most impactful research, but the things where I know the struggle that went into solving the puzzle that was in front of us,” he explained. “The thrill of the chase may not be as interesting to the rest of the world but you know how hard that person worked and how many false leads there were.”

Recently, Burke has expanded his passion for motivating others to a new area. In July, Burke became the Interim Chair of Molecular Microbiology & Immunology.

“Now that he’s the interim chair he is trying to provide the same kind of supportive environment for the department that he’s been doing for his lab,” Pintel said.

Burk said he wants to help other faculty members achieve their goals and prioritize tasks. He is also involved in a new faculty search where he works to ensure the applicant pool reflects those that might be wanting to apply by removing language that may prevent people from applying.

“Again, I want to help find what obstacles can be in their way and get rid of those before it slows them down,” Burke said restating his passion for helping others achieve excellence.

Donald Burke-Aguero is an MU professor in the Department of Molecular Microbiology & Immunology. He received his bachelors’ degree from the University of Kansas and his Ph.D. from the University of California, Berkeley. Burke joined the MU community in 2005.

#IAmScience Paige Gruenke

July 6, 2017 By Mary Jane Rogers in #IAmScience Tags: aptamers, biochemistry, HIV, RNA

By Mary Jane Rogers | Bond LSC

“#IAmScience because I am fascinated by life on a molecular level and inspired that my research could positively impact medicine.”

As a graduate student in Donald Burke’s lab at Bond LSC, Paige Gruenke explores the role of ribonucleic acid, or RNA. That means her work involves a lot of test tubes. She looks at how specialized RNA molecules, called aptamers, bind tightly and specifically to proteins from HIV to prevent the virus from replicating. Her job is to locate the aptamers that bind to HIV proteins from a very large starting pool of RNA sequences by doing repeated cycles of removing the sequences that don’t bind and keeping the ones that do, until the strong binders dominate the population.

“A lot of the things I do don’t sound very exciting,” said Gruenke. “It’s throwing components into tubes and waiting for things to happen. It might sound mundane, but it’s all for the greater good.”

Gruenke hopes that her research will give scientists a better understanding of HIV, because understanding the virus will lead to better drug treatments and eventually, a cure. She is finishing up her second year as a Ph.D candidate in biochemistry, and plans to graduate by summer 2020. Gruenke has always been interested in the area of molecular medicine, but she has some advice for students who are just getting started.

“On a day to day basis, many experiments fail,” said Gruenke. “You’re always going to be learning something you didn’t know before. So, don’t be disheartened because something didn’t work out — just keep trying. Because whenever you have an ‘Aha!’ moment, it makes it all worthwhile.”

Building blocks of life in the lab could revolutionize life for us all

September 2, 2016 By Roger Meissen in Research Tags: Bond LSC, exobiology, mizzou, NASA, RNA

NASA, NIH-funded work seeks to understand bio-chemical mechanisms of life on Earth, and among the stars

By Phillip Sitter | Bond LSC

Any child obsessed with Legos knows the fun of creation bound only by imagination and the size or variety of the blocks within their pile.

For some scientists, that spirit extends into adulthood, but instead of plastic parts they think about arranging blocks of nucleic acids.

Scientists may not be able to create dinosaurs, dragons or mythical sea creatures the way kids with Legos can. Through the manipulation of nucleic acid building blocks though, they may be better able to understand how the processes of life on Earth work, as well as out among the stars.

“I have a lot of fun asking what is possible,” said Donald Burke, a Bond Life Sciences Center investigator who spends his time researching the building blocks of life.

Burke said he has been interested in the origins of life for 40 years, and he has been associated with NASA for about 20 years.

NASA’s interest in understanding the origins of life is pretty straightforward. It wants to know what clues to look for on other worlds to figure out if those planets also support life.

Many of Burke’s previous discoveries at Bond LSC are funded by NASA’s exobiology and evolutionary biology program.

“No, I have not thought of an excuse to fly anything up there. I’ve tried to think ‘which of my experiments would make sense to do in a micro-gravity or zero gravity environment?’” he explained of the prospect of sending some of his work into orbit, with a wry smile.

But, there’s even more to understanding the building blocks of life than looking for bio-chemical signatures out among the stars. Knowing how these parts are put together allows scientists like Burke to understand the origins and processes of Earth’s biology, and, conceivably create chemical and biological processes or even organisms not found in nature in the near future.

A quadrillion arrangements of blocks, one arrangement at a time

“Many of the molecules of life are built from strings of amino acids, or nucleotides or other building blocks,” Burke explained. He also noted that these buildings blocks are not just strings, but fold up into three dimensional shapes.

RNA, or ribonucleic acid, stands out as an essential building blocks in the bio-chemical processes of life.

Put simply, RNA is a kind of molecular structure of nucleic acids similar to DNA (deoxyribonucleic acid) that comes in many combinations. These combinations are at the core of every cell, and play a role in coding, decoding, regulating and expressing the basic operating instructions for each cell — its genes.

The molecules we’re talking about are almost unimaginably small. In one test tube, Burke said there can be one quadrillion of them — that’s a one with 15 zeroes after it. Put another way, that’s roughly equivalent to the estimated number of ants that live on Earth.

Burke’s work focuses on the end goal of being able to artificially create original RNA combinations. In what’s known as experimental evolution, “the population of molecules in the tube is evolving as a result of us imposing experimental constraints upon it.”

This artificial synthesis of RNA molecules looks to create random sequences or variations on natural RNA to create new ones non-existent in nature. A second route aims to selectively choose molecules with certain properties, and use them to build altogether new combinations.

“Their string-like properties allow us to copy them, and make more copies, and make more copies, and make more copies. Their shape-like properties allow us to observe the bio-chemical behaviors they may have,” Burke explained how he and other scientists interact with RNA’s structure in the lab.

“I don’t think we know what those limitations are yet,” he said of the capabilities of RNA.

The motivation for wanting to be able to intentionally design RNA molecules is so that it “can do the things we want it to do under the conditions where we want it to do those things,” he explained of the process of the process of selecting RNA sequences for specific properties.

“I want the ones that will bind a tumor cell. I want the ones that will bind a viral protein. I want the ones that will catalyze useful chemical reactions.”

RNA’s path to the future following in biology’s footsteps

The National Institutes of Health and other organizations recognize that engineered forms of RNA have the potential to fight diseases, and they have funded Burke’s work.

He has studied RNA that instructs human cells on how to defend themselves from HIV and is now looking at other RNA that interferes with the proteins of the Ebola virus.

The expectation is that such therapeutics would work in conjunction with other treatments. In the future, they could be expanded to help fight other viruses, cancers and other diseases.

RNA could also be used to start, or catalyze, chemical reactions. As Burke explained, catalysts remove barriers to chemical reactions — “they don’t make things happen that wouldn’t otherwise happen, but they speed up the process.”

Synthetic RNA could be used to accelerate removal of toxins from soil or to get the bacteria in our guts to recognize cancerous tumor cells and kick-start an immune response.

But, the future of RNA research may soon reveal a few different Holy Grail moments on its horizon.

One such Holy Grail that Burke said will definitely happen will be observations consistent with the presence of life on other worlds, based on evidence like an atmosphere having certain chemical compositions.

Another likelihood could involve construction of a self-replicating, fully-artificial organism, either created from scratch or reverse-engineered from other organisms.

For those of you already anticipating the plot of a low-budget sci-fi thriller, Burke offered to assuage your fears.

“The notion of it escaping out in the world and taking over Los Angeles is [only] good 1950’s B-movie” material, because the conditions under which this artificial organism would survive would probably be difficult to maintain even in the controlled environment of lab, he said.

Instead of B-movie science, Burke explained that “really, I’m thinking about what kinds of chemistries we want to see take place, and then building the enzymes that would make it possible.”

“Biology has had a few billion years to work on this, but we’re just starting to figure it out.”

Donald Burke-Agüero is a professor of molecular microbiology and immunology and joint professor of biochemistry and biological engineering.