“#IAmScience because the lessons I learn through research will help me to one day become an astronaut.”
Asking kids what they want to be when they grow up usually leads to a variety of answers: doctor, lawyer, president, astronaut. A few years down the line, though, most of those answers change.
Chris Zachary, a junior chemistry major, is the exception. He never outgrew the dream of being an astronaut and is involved in science, technology, engineering and mathematics (STEM) with going to space in mind.
“There isn’t a clear path to becoming an astronaut, but I was advised to stay in STEM,” Zachary said.
While his ultimate goal requires some extreme preparation and travel, Zachary keeps himself involved to make that dream a reality. Right now, he works in the Mendoza lab at Bond LSC, which he found through his involvement with Mizzou’s Initiative for Maximizing Student Diversity (IMSD).
“I knew I was interested in science and that I wanted to do something with chemistry,” Zachary said. “During an IMSD meeting, Mendoza came in and talked about what his lab does. I was interested, so I pursued it.”
The opportunity to do something a bit outside of the norm was appealing to Zachary because it helps to diversify his experience as a researcher and a student.
With two years under his belt in the Mendoza lab, Zachary now works to uncover some weighty issues in plant cells.
“Our lab focuses on heavy metal transporters, specifically iron,” Zachary said. “One of the most common forms of malnutrition around the world is anemia, and one of the best ways to fight it is to make more nutritious crops.”
That process is called bio fortification, and it allows plants to be more efficient at absorbing nutrients, which will help to alleviate world hunger.
When he’s not working to feed the world, Zachary’s dreams of blasting off to Mars consume him.
“There’s a lot that goes into being an astronaut, like a height requirement and physical tests, which is pretty daunting,” Zachary said. “In the end, though, it’ll be worth it.”
However, in the meantime he wants to maximize his experiences at Mizzou.
“[When choosing a lab] I didn’t want to close myself off,” Zachary said. “Working here helps me because instead of a narrow field, I chose the broader path. I can say I’m a chemistry major who worked in a plant sciences lab, which is huge.”
Purva Patel grew up captivated by newspaper articles discussing a method to grow plants without soil called hydroponics.
Today, she is one of the scientists mixing the mineral and nutrient solutions to plant seeds in this rapidly growing soil-less method.
The University of Missouri senior spent the past year working in David Mendoza-Cózatl’s Bond Life Sciences lab. Her research, which started out as a capstone project, has now turned into a pastime.
“I learn something new every day,” she said. “I did not know much about plants before joining this lab, but now I just love how all this is working at the genomic level, and I’m really very interested in understanding at what’s happening at the core of the plant.”
Patel studies how plants accumulate iron in the model organism, Arabidopsisthaliana. Iron is an important metal that provides nutrients humans need to perform important cellular processes. Plants are the primary source of iron and other essential micronutrients for humans and livestock worldwide.
Plants receive iron from the soil and transporters distribute iron from the roots to the rest of the plant. Most of the transporters involved in keeping the levels of iron balanced are not known; that’s where Patel comes in.
She started with more than 20 different Arabidopsis seed lines. Each seed line disabled a different gene, causing a loss of function that might be responsible for the movement of the metal into and out of cells.
The seeds were placed in different dishes with artificial soil that emulated real soil conditions. Some had regular levels of iron while others had an excess or deficient amount. Next, it’s time for them to grow. After they grow, she measures the roots and shoots and compares them to the wild-type plants that signify normal growth.
She narrowed down the potential genes to three seed lines. Those three types of seed lines were selected because they grew different than the normal plants and showed consistency in displaying the same leaf color and lengths of the shoots and roots.
For Patel, this step was the most exciting,
“Even in the absence of iron, the mutated plant has longer roots and the wild type does not, so I think the very visible difference between those would be the biggest thing I have come across.”
Now she wants to know the amount of other essential metals, like zinc and copper, that accumulate in plants’ tissues during various growing conditions with or without iron. For this, she uses a machine called ICP-OES (Inductively Coupled Plasma Optical Emission Spectrometry). The machine detects and measures metals in a plant sample. The results from ICP will help Patel determine how the mutants accumulate elements differently than the wild-type.
Patel explained her work is only one step in the process to understand the mechanism. She hopes her findings could produce more nutrient-rich crops someday.
“It can be nothing,” she admitted. “There is a chance, but I want it to be something.”
Whether she finds something substantial or not, Patel hopes to use her knowledge of genetics she gained in the lab to get a master’s degree in the biomedical field.
“It’s great that the science we learn in the classrooms is not only limited to there, but we get to apply it here and see the results and try to make the world a better place by using that knowledge for practical uses,” Patel explained.
Computer scientists create applications to speed up research in the lab
By Samantha Kummerer, Bond LSC
Three years ago, Ke Gao stood uncomfortably beside rows of biomedical students and plant scientists at the Bond Life Sciences research fair. His poster wasn’t discussing the DNA of seeds or how plants transport nutrients but rather a scientific device.
“At the beginning, the visitors didn’t understand what we were presenting, but once I explained how our application can help them accelerate their research and how we can really turn their phones into a research device, they got really excited,” Gao explained.
Gao’s presentation highlighted a mobile app that transforms images of seeds into objective, quantitative data.
It started with a simple problem. Plant scientists were manually comparing hundreds and in some cases thousands, of seed photos. The process was meticulous, slow and subjective.
The solution began with a collaboration with Michele Warmund (Plant Sciences), Tommi White (MU Electron Microscopy Core) and Filiz Bunyak (Computer Science) that led to a MU Interdisciplinary Innovations Fund grant.
Gao was part of this team that developed an algorithm to turn the photos of seeds from the field into data with the touch of the button.
Gao explained the app is very similar to Instagram.
A user takes or uploads photos of seeds. Then the app calculates measurements describing shape, color and size characteristics of the seeds. This data can be emailed or stored in a database.
Some experiments need thousands of seeds analyzed; this would be a massive feat for even a group of students. With this app, hundreds of seeds can be photographed and measured from a single photo. The app analyzes each seed individually and also computes measurement averages for groups of seeds.
There are other apps that analyze seeds, but this is the first mobile application as far as the team knows. Its ability to analyze multiple seeds at once, even if they are touching is also an outstanding ability. Bunyak’s previous experience developing applications to quantify microscopy images and videos of touching and clumping cells helped them design the algorithm to make that function possible.
This isn’t just a problem for researchers in this one lab or even at the University of Missouri.
MU Computer Science professor, Filiz Bunyak, said noninvasive methods to observe and understand biology, imaging equipment and corresponding computing devices have advanced considerably in recent years, leading scientists to produce large amounts of data. The ability for researchers to analyze and quantify this large amount of complex and unstructured data, however, was still missing. Bunyak said this app began as a project to advance scientists’ capabilities to automatically analyze image-based plant phenotyping.
Bunyak and her students are advancing the field of high-throughput phenotyping beyond this mobile app.
High-throughput phenotyping (HTP) refers to the process of connecting an organism’s DNA makeup to its physical characteristics; it is also a hot topic buzzing through the science community in the last five years.
Two years ago, Bond LSC scientist David Mendoza, who studies how plants collect nutrients, said he never imagined he would be doing HTP.
“The old way of doing this is growing plants on plates and, I’m not kidding, with a ruler you measure how long the roots are,” Mendoza explained of the traditional process that now seems archaic.
Now, the lab is working with computer scientists to design a robot to code the measurements for multiple roots at a single time. For a student, it would take 15 minutes, but now it’s complete in an instant.
Speed isn’t the only reward researchers are reaping.
Bunyak said computational image analysis allows researchers to come up with new ways to quantify and study data that they were not even able to do before, leading to the design of novel experimental methods.
Ruthie Angelovici is another Bond LSC researcher who uses computer scientists to aid in her research.
She said without computer imaging there would be no way for her team to do research that measures plants physical and biochemical traits. Angelovici’s lab uses Bunyak’s mobile app system but on a computer. Eight plants are photographed at once and the application keeps track of features of plants such as shape, color and area as they develop.
What is really revolutionary to Angelovici is the ability for the data of plant growth parameters to be stored and revisited without the need to re-grow. This contrasts with past experiments where researchers would scribble some notes and never be able to return.
“It’s not lost and I think that’s a big step in this field,” Angelovici said.
The collaboration is creating more than advanced tools by fostering a new way to think and approach research.
Rather than buying pre-existing software, the groups from Bond LSC utilizes the resources on campus to build their own devices.
“I would have been in front of a black box that is doing things for me and that would not have given me the tools to teach to my students,” Mendoza reflected. “Now I know what they need to learn to be competitive. Now I know what the gaps are and how they can be filled. I think that was worth it.”
Angelovici compared it to buying a cake versus making a cake — at the end of the creation process, she said she would have the knowledge to do a lot of other experiments.
This new way of thinking already began to pay off this summer when her lab expanded computer software to analyze seed size.
“We only approached it because we saw how things worked together. I just pitched a project to engineering about seed collector. Again, this opened my eyes that even undergraduates can do something not so difficult for engineers, but I have no clue how to do it,” Angelovici said.
Mendoza agreed the collaboration is exciting but challenging, “You got a Ph.D. and you got a faculty position and you think you know stuff. When I started this I realized how much I don’t know, but at the same time it reminded me that it is really cool to learn something new.”
Both teams continue to work towards maximizing the functions of their individual machines, but even after the projects reach fruition the collaboration will not be over.
“On the contrary, I think we’re going to keep building more and more and better,” Mendoza said.
Nowadays, Gao no longer feels out of place at the Life Sciences fairs. Researchers from various labs come up to him and ask how they can implement his app in their own lab.
“It seems like I’m doing something that can really help people, so that’s the best part of this process,” he said.
Ruthie Angelovici is an assistant professor in the Division of Biological Sciences and is a researcher at Bond Life Sciences Center. She received her degrees in plant science from institutions in Israel — her B.S. and M.S. from Tel Aviv University, and her Ph.D. from the Weizmann Institute of Science in Rehovot. She was a postdoctoral fellow at the Weizmann Institute and at Michigan State University and has been at MU since fall of 2015.
David Mendoza is an associate professor in Plant Sciences, Life Sciences Center investigator and a member of the Interdisciplinary Plant Group. His research focuses on the mechanisms plants use to resist toxic elements or acquire nutrients. He received his Ph.D. in biochemistry from UNAM in Mexico City and continued on to do post-doc training at UC San Diego.
Filiz Bunyak is an assistant research professor in the Department of Computer Science. She received her bachelors and masters degree from Istanbul Technical University and her Ph.D. from the University of Missouri- Rolla. Her work focuses on computer imaging, image processing, and biomedical image analysis.
Ke Gao is a doctoral student in the University of Missouri’s Department of Electrical Engineering and Computer Science. He earned his bachelor’s of science from the Henan University of Science and Technology in China.
“#IAmScience because it’s fun. You’re paid to work with exotic materials and instruments to solve problems that drive at how life manifests.”
Samuel McInturf’s father is an accountant and his mother is an HR director, but somehow he ended up falling in love with science. By the 4th grade he had already asked his parents to buy him a compound microscope. He completed his undergraduate degree in plant biology at University of Nebraska, Lincoln with a minor in biochemistry. Now, he’s finishing up his fifth year pursuing a Ph.D in plant stress biology and works in Dr. David Mendoza-Cózatl’s lab at Bond LSC.
“I mainly came to Bond LSC to work with Dr. Mendoza,” said McInturf. “The work in his lab was right in line with what I wanted to do and I knew the faculty at Bond LSC was great.”
And he’s enjoyed the last five years he’s spent here.
“Bond LSC has vast resources of knowledge and labs are very friendly towards one another,” he said. “So if you are short up on a reagent, or you need to learn to do an assay, someone is always available to lend a hand.”
McInturf’s thesis deals with understanding the genetic factors that balance the uptake and demand for micronutrients – heavy metals – against their toxicity. He specifically looks are regulators of iron and zinc homeostasis.
In addition to his interest in plant biology, he’s also an engineer of sorts. McInturf helps teach a bioengineering class at Bond LSC with undergraduates. The goal of the class is to build robotics that aid laboratory research, and he has taught three of these classes so far.
“I found the change in scale between building widgets in my bedroom to building full scale devices challenging, but ultimately rewarding,” he said.
For undergraduates interested in continuing a career in science, McInturf advises them not to give up, even when things get tough. He admits that he was intent on dropping out of school up until he was 18, but now he’s almost finished with his Ph.D.
“Ten years ago I was very intimidated by what I saw as the difficulty of science and was wavering on whether I wanted to take the dive into a research-heavy field,” he said. “It took a few years to figure that out, so I guess I would have told myself to get a move on and not be so faint hearted about it.”
McInturf isn’t positive where he’s like to be in 10 years, but he’d enjoy continuing to teach and conduct research at a university like MU.
“I’d love to have Dr. Mendoza’s job one day,” he laughed.
Researchers in the Mendoza-Cozatl lab grow beans in a soil that simulates Martian soil By Eleanor C. Hasenbeck | Bond Life Sciences
As NASA works to send people to Mars, researchers at the Mendoza-Cozatl lab at Bond Life Sciences Center are exploring the possibility of sending beans to the red planet. The journey from Earth to Mars alone would take somewhere between 100 to 300 days. To feed astronauts on these longer missions, scientists are studying space horticulture.
Norma Castro, a research associate in the lab, studies how common beans grow in a soil that simulates Mars’ red soil. The common bean is a good candidate for interstellar cultivation. Beans are a very nutritious crop, and their affinity for nitrogen-fixing bacteria can improve soil health while requiring less fertilizer. Castro is trying to understand how different varieties of beans could grow in the soil.
“This kind of research not only will tell us the right plants to take to Mars, but also which kind of technology needs to be developed,” Castro said.
Nga Nguyen hopes to apply her research to increase nutrient contents in crop plants
By Eleanor C. Hasenbeck | Bond LSC
Plants smell better than animals, at least to Nga Nguyen. That’s one reason why she decided to study them.
“In my undergrad, I studied horticulture,” Nguyen said. “For that you don’t really learn the inside mechanisms of plants, so I decided besides knowing the cultivation techniques, I’d like to also learn about the molecular biology.”
As a fifth year doctoral candidate in the Mendoza-Cózatl lab at Bond Life Sciences Center, she hopes to combine her undergraduate background with her present research in the microbiology of plants to improve the crops of the future.
Nguyen studies how transporter proteins move micronutrients like iron through plants. By understanding how plants move these nutrients in model plants, researchers hope to apply the same understanding and techniques to crops like soy and common beans. Increasing the micronutrient content of these crops could be a useful tool in combatting nutrient deficiencies in areas where people don’t have access to meat and dairy.
But Nguyen says the benefits of studying plants don’t end there. “I hope people pay attention to plant research and study,” Nguyen said. “If you think about it, it’s not just our food, but our clothing and the materials we use.”
That was the case in what led to a new collaboration between the Mendoza and Peck laboratories. The two researchers were recently awarded $48,250 in seed money from the Bond Life Sciences Center to adapt a new technology to the study of signaling pathways in plant cells.
David Mendoza, a Bond LSC researcher and assistant professor of plant sciences who is interested in nutrient uptake in plants, got the idea for the project when he attended the Trace Elements in Biology and Medicine conference in June. There, he kept hearing about an enzyme called BioID used to identify protein interactions in mammalian cells.
“In plants, we have a hard time figuring out how proteins interact with each another to transfer information within the cell,” Mendoza said. BioID could be the key.
BioID works like a spy slipping a small tracker into the coat pocket of every person it encounters, but instead of a tracker, BioID transfers a unique molecular tag onto every protein that comes near. It’s a speedy process, no matter how brief the interaction between BioID and the incoming protein. But once the proteins are tagged, they can be rounded up and identified later, even if they’ve moved elsewhere in the cell.
Scientists can study which proteins interact with their protein of interest by linking BioID to their protein. This lets them track the signals being communicated to and through their protein without disrupting what’s happening inside the cell.
Although BioID has exclusively been used in animal systems, Mendoza talked to the scientist behind BioID to see if it could be used in plants.
Incidentally, BioID has been publicly available for several years but the enzyme was impracticable for plant experiments. It needed a lot of raw material on hand before it could start tagging proteins, much more material than what is normally found within plant cells.
However, research on a more suitable candidate called BioID2 was published just months before the conference. Unlike its predecessor, BioID2 required very little starting material to function in plants.
“Like a lot of things,” Mendoza said, “timing was key.”
When he approached Scott Peck, a colleague at the Bond LSC and professor of biochemistry specializing in plant proteomics, with the news, Peck saw immediate applications for BioID2.
With currently available methods, plant scientists have to look at protein interactions in artificial environments, such as in a test tube or in yeast systems. A real-time protein-tagging method would allow plant scientists to observe signaling pathways in their native environment–the cell–under a variety of conditions.
“It allows the contextual information within the plant to still be present,” Peck said.
For example, with BioID2 the Peck lab, which studies plant resistance to bacteria, could watch how incoming stimuli such as plant pathogens or stress from drought affect overall protein-to-protein interactions within plants, compare these protein interactions across different cell types, or even discover previously unknown protein interactions, he said.
“You know you have a good idea when the other person gets excited right away,” Mendoza said.
Peck also had a suitable model handy in which they could test BioID2 at work, but the two researchers first had to make sure plant cells could produce functional BioID2. Mission accomplished, the next step is to make plants produce BioID2 that is linked to their protein of interest.
“The nice part of this seed grant is it lets us get a jump on some new technology to develop here,” Peck said.
Using BioID2 in plants is an interesting and novel idea, Mendoza said. “For me, that’s enough to try.”
This seed funding is one of seven awarded this year at the Bond Life Sciences Center. These awards, which range from $40,000 to $100,000 in funding, foster inter-laboratory collaboration and make possible the development of pilot projects.
Forget fruits and vegetables, seeds provide a critical part of the average person’s diet. From beans to cereal grains, understanding how genes and soil types impact nutrition could one day help produce more nutritious food.
One University of Missouri researcher wants to know which genes control the elements in these nutrient-rich packages.
“Iron and zinc deficiencies are considered two major nutritional disorders in the world, so there’s a lot of interest in developing plants with enhanced amounts of these micronutrients,” said David Mendoza-Cozatl, a Bond Life Sciences Center plant scientist. “The question for labs like mine is how can you convince a plant to accumulate more of these metals even though high concentrations can be toxic to plants?”
In a five-year collaboration with researchers at the University of Nevada and UC San Diego, the group measured the amounts of 14 elements in both plant seeds and leaves of mutant Arabidopsis thaliana plants planted in different soil types (salty, alkali, heavy metal and normal).
These mutants were special. Each plant had a different gene disabled, allowing researchers to tell if the disabled gene affected uptake of minerals into the seeds or leaves.
The teams found that 11 percent of genes influence proteins relevant to the nutritional content in seeds. Soil types also played a role in the significance each gene’s impact.
The approach could be likened to understanding how a car works.
“What we are doing here is we have a car with different parts missing, and the question we are asking is what happens to the car without each of these parts,” Mendoza-Cozatl said. “In plants we ask how more or less elements or nutrients can accumulate without each of these parts, these genes. That’s how we are trying to assign the function of a gene to nutrient homeostasis.”
Mendoza-Cozatl’s work with the group focused on soil laced with non-essential heavy metals (e.g. cadmium and arsenic). They grew mutant plants from seeds and compared nutrient content of those plants’ leaves and seeds to a baseline. To do this, researchers “digested” leaves and seeds, separately, then quantified the amounts of elements.
“We turn everything into basic elements by putting the seeds or leaves in a tube, adding nitric acid and boiling them,” Mendoza Cozatl said. “We found that the mineral makeup of the seed and leaves can be different.”
This surprised him since nutrients in seeds come through the leaves via the phloem. The phloem is living tissue that transports nutrients throughout a plant.
Nutrition isn’t the only area that could benefit from knowing what controls the transport of minerals in plants.
A newly engineered plant could be made to use less fertilizer or move particular types of minerals, like toxic heavy metals.
“Many former industrial areas contain fields contaminated with heavy metals like cadmium and arsenic,” Mendoza-Cozatl said. “Understanding genes important to nutrient transport could help both with bioremediation in soil and bio fortification in food.”
Genes identified through this study will lead to new research in the Mendoza lab as well as other labs involved in this large project.
“The mechanism underlying these changes in nutrient seed composition are not known, so we still need to find how these genes are affecting the seed composition,” Mendoza said. “That’s where the advance will be more significant, and we’re not there quite yet.”