The greenhouse isn’t a place most researchers linger. With condensation sticking to the glass windows, scientists usually don’t dawdle longer than 30 minutes in the heat and humidity. But Dangping Luo, on the other hand, doesn’t seem to mind and takes his time tending to his rice plants.
A research scientist in the Bing Yang lab at Bond Life Sciences Center, Luo, is a man of determination and conviction. For the past 18 years, Luo has been studying rice genetics and its interaction with disease.
“When I think something is of importance, I never give up,” Luo said.
Luo was working as a teacher in Southern China when he found his fascination for rice genetics. Luo went on to complete his Ph.D. at the South China Agricultural University in 2013. He then moved to Iowa with his family for his post-doctorate at Iowa State University, where he joined the Yang lab. Luo followed Yang to Bond LSC in 2018.
Although he was offered a professor position at a university in China, he turned it down in lieu of finishing his work at Bond LSC. The position is still open for him.
Part of that work continues to be published this year. Luo published a paper in January describing how the Xa7 resistance gene in rice protects the SWEET14 gene that is susceptible to a major disease for rice, bacterial blight.
“We hope that we can elucidate the mechanism and explain the resistance,” Luo said. “[This gene] may help us understand other genes better and can usually help us breed good rice.”
Luo found that Xa7 is an adaption in rice that has emerged to counteract efforts by blight bacteria pathogen infection.
Luo’s 20 years of knowledge about rice comes in handy in the lab.
“I regularly ask him basic questions. I think he knows everything,” said Chenhao Li, visiting student in the Yang lab. “He’s really an expert on rice development and pathology, so it’s very nice because he has much more knowledge than me since I’m a student.”
Li met Luo three years ago at Iowa State University and has seen for himself Luo’s dedication.
“If you keep those plants healthy, they will give you great results,” Li said. “He just takes care of rice like it’s his baby. We usually take soil from the field, there are many impurities, but he would just totally clean the soil to prepare for the rice.”
Luo is proud that he’s been able to uncover many important rice genes and won’t stop until all his questions are answered.
“I really enjoy doing such work, even when it’s very hard,” Luo said.
As someone interested in getting a Ph.D., you apply to several schools and programs hoping to get in.
When Lauren Jenkins first interviewed with Mizzou, she knew it was the one. But the interview was not the first time she’s had a good impression with the school.
As an undergraduate student at the University of Missouri-St. Louis, Jenkins’ first science conference was the Interdisciplinary Plant Group (IPG) Seminar at the Bond Life Sciences Center.
“I actually had the opportunity to give a talk there,” Jenkins said. “I just remember being an undergrad and I was so intimidated, but it actually turned out really well. I had some cool conversations there and no one made me feel unimportant, people were really interested in it.”
Now a Ph.D. student in the Ruthie Angelovici lab, Jenkins got started in January and has hit the ground running.
“I’m very impressed with her ability to interpret the biology and how quickly she’s getting the hang of things and contributing creative ideas,” Angelovici said. “It can be a bit overwhelming, so I really appreciate how well she’s integrated in and I think she’s bringing a lot of analytical perspective that is very needed in the lab.”
Jenkins works on several projects in the lab.
Her main two focuses look at changes in the protein metabolism in maize under drought conditions to see how the proteins balance themselves after a large change.
In addition, she engages in research approaches that will lead to identification of high priority candidate genes in maize and Arabidopsis, that can potentially change protein quality in seeds.
“Plants are awesome for that because every plant has its own metabolism going on,” Jenkins said. “There are endless possibilities to what you can research in that regard.”
Plant metabolism is important because it comprises pathways that are essential to plant growth, regulation and has a large impact on the development and survival of the plant.
“It is really cool,” Jenkins said. “I’ve never been involved in big genetics projects and to see how those can be fruitful is really cool. I’ll also get to do some really cool molecular work on them that I also haven’t done before, and it will be fun to take those forward.”
Jenkins’ previous experience comes from the Donald Danforth Plant Science Center in St. Louis, where she was an intern.
“My work at the internship really gave me a lot of skills,” Jenkins said. “I worked with some mass spectrometry while I was there, which is some of the skill sets that we use in the lab here. One big thing for me is that I already know how to do this and it’s good because they both look into metabolism.”
This experience helped her jump right in to the Angelovici lab.
“She brings a fresh perspective,” Angelovici said. “She has a lot of background in analytics and now she’s learning to integrate her analytic skills with the system biology that we are doing. It’s very early days for her, but she’s showing a lot of promise.”
Two months in and Jenkins is happy with her choice to come to Bond LSC.
“The plant science community is super great,” Jenkins said. “It’s kind of close knit and I really enjoy the interactions that I get. Even big-name PIs are really personable and love talking about their science with you, which is really nice.”
Cynthia Tang and Henry Wan | photos by Becca Wolf and Roger Meissen, Bond LSC
By Becca Wolf | Bond LSC
You would think that the less sick you are, the less contagious you are. That’s just logic.
However, science isn’t always logical. Especially with Covid-19.
Henry Wan, principal investigator at Bond Life Sciences Center, recently found that when a person has mild symptoms of Covid-19 they have a higher amount of viral shedding.
He also found that people with a higher amount of virus on their positive swab test are less likely to be hospitalized than those with a lesser amount.
“We are really interested in whether this may be causing more or less hospitalizations, and we found the opposite in the analysis,” Wan said. “We found that viruses that mutate a certain way can make the disease less severe. We then wondered if there are any [particular] mutations that cause this.”
Wan and his lab decided to look at different Covid-19 mutations. Using positive Covid-19 tests from throughout Missouri, they found four local lineages and several mutations. With this information, they analyzed patient data to see how people are reacting to each mutation.
“We need to understand how the community gets the mutation and how it spreads,” Wan said. “We want to understand this very dynamic process in Missouri. We’ve seen a lot of mutations introduced in the past several months. Some of them continue to spread and some of them die. We want to know what ecology factors cause this.”
Cynthia Tang, a M.D. Ph.D. student in Wan’s lab, helped with the research. She did work on the data collection and performed the analysis.
“Within the first eight months in Missouri alone we identified four new lineages, which shows just how quickly the virus can mutate and spread,” Tang said. “We also found that viral load was increasing over time. That in itself was very interesting.”
They then looked at if the specific lineages were associated with the increase in viral load but did not find any conclusive evidence. As a result, they speculated that there may be an overall selective advantage towards more viral load and viral shedding, but then found that an increase in viral load was associated with decreased severity.
Given how novel Covid-19 is, they knew they had to expect anything. From the past experience on influenza pandemics and throughout pandemic outbreaks, viruses typically evolve to adapt to the human population, to be less severe while spreading more readily to become seasonal.
“It was challenging going into the research without a lot of information,” Tang said. “There are a lot of publications out there, but our overall foundation of this virus and the disease itself isn’t that strong yet since the pandemic just started, so it’s challenging trying to figure out what the right questions are.”
Wan used this as a teaching moment.
“In the past, we are taught about pandemics in a textbook and that they are far away from us — like the 1918 flu. But now, we’re in it,” Wan said. “This is a good opportunity to lead them through real situations. I’m sure when the students grow up and maybe become a professor or a scientist in the future, they will be ready to fight the next pandemic when it comes.”
As a student, Tang has learned a lot; she has never worked on a project quite like this.
“It’s been a really interesting experience because this is my first time working on something that has a pressing timeline,” Tang said. “We need to get answers quickly because it’s causing so much damage. You’re learning about it, and you’re discovering new things with everybody else.”
Wan and Tang are grateful for the learning experience and the findings of this research.
“This study gives us a better understanding of how the virus is adapting,” Tang said. “But I think it’s good news that the pathogenesis is decreasing for disease severity.”
Social media botany advocate and self-proclaimed coffee snob, Shawn Thomas is the kind of person to find joy in everything.
Thomas graduated from the University of Georgia in spring 2018 and worked as a bioinformatics technician for a year with Jim Leebens-Mack before joining Chris Pires’ lab at Bond Life Sciences Center as a Ph.D. student in fall 2019. Ever since, he’s been studying how genome duplications affect plant traits in a certain group of plants that include broccoli, cauliflower and kale.
Genome duplications occur when DNA is copied multiple times in a plant when two species hybridize and come together. To study this, Thomas is looking at their wild distant relatives.
“Understanding these ancient genome duplications, how they happened and when they happened can give us an idea of how different evolutionary innovations occur,” Thomas said.
Thomas has been a part of the Pires lab for over a year now and has brought his own set of skills.
“The thing that I’ve been really impressed with him — well, two things — one is he’s very skilled with bioinformatics,” said Pires, Bond LSC principal investigator. “He doesn’t have a computer science degree, but he’s got math skills and coding and a couple of different computer languages for data wrangling genomes. But the other thing is he’s made some really hilarious YouTube videos.”
Mixing his love of plant biology and lab inside jokes, Thomas makes clever YouTube videos for fun and even for grants.
One video includes what it’s really like inside the Pires lab, despite Pires’ expectations. It involves a well-known lab joke about Thomas prioritizing his undergraduate work while putting aside his Ph.D. thesis.
Another video acted as a submission for the PACBIO 2020 Plant and Animal Sciences SMRT grant program. The video was about the need for a reference genome of Cakile — “Sea Rocket” — to enable new studies in polypoid evolution, plant migration and crop improvement. In Europe, arugula is known as “rocket,” and a closely related species to rocket is “Sea Rocket,” so Thomas didn’t miss the opportunity to have some fun with it.
Even outside of YouTube, Thomas is tech-savvy on many fronts.
“I like to play with computers, and I like genetics, so playing around with big data genomic data has been fun,” Thomas said. “The work that I do is more basic research, where we are trying to understand the fundamental concepts behind how plants work and how these different mechanisms work. For me, the curiosity of trying to understand how polyploidy works is what interests me.”
Thomas is active on Twitter talking about everything Brassica — the mustard family — to help get others engaged in the basic research of plant biology.
“When we go to a conference, I’m known for being too much of the Twitter guy, but he’s also in there tweeting all the talks,” Pires said. “So, he’s not afraid to be an advocate for botany. He clearly loves botany, and he wants to have an influence, not just a science influence but an educational outreach kind of influence.”
In the lab, Thomas often helps move things forward by reminding the group about journal clubs, reading papers and corralling the undergraduates through his love of coffee.
“I’m a bit of a coffee snob, so I like to experiment with coffee and try all the new different recipes and techniques,” Thomas said.
Before the pandemic, Thomas would regularly visit Shortwave Coffee and get a pour-over of Ethiopian coffee (he highly recommends it). Now, he makes his own each morning and talks with the undergraduates about coffee while distanced in the lab.
“He’s a good team player, and he’s very social,” Pires said.
While Thomas is still learning how to be a mentor and exploring the diversity of plants, he has even more ahead of him.
“I’m proud of what I’ve done so far,” Thomas said. “I definitely have a long way to go, but I find enjoyment out of being able to create a nice figure or graph or get a good result that works with the story that we’re trying to tell.”
As part of an international collaboration, principal investigator Wes Warren helped study capuchins in Costa Rica. | Photo contributed by Amanda D Melin, Bond LSC.
By Lauren Hines | Bond LSC
Through monkey poop and three years of work researchers from all over the world sequenced the Panamanian white-faced capuchin genome for the first time and devised novel methods to sequence many more wild capuchin genomes.
These monkeys have large brains for their small size and can live past 50. Wes Warren — Bond Life Sciences Center principal investigator — helped sequence the genome to find more answers about their unique brain-to-body ratio and long lifespans as part of the study. This work published Feb. 16 in Proceedings of National Academy of Science looks deeper at the genetic connections to these adapted traits.
“Other species of nonhuman primates don’t have that long lifespan, so the capuchin is a nice model and a different group of nonhuman primates to study that question,” Warren said.
Warren first got involved in his previous job at Washington University in 2017 when Amanda Melin, former principal investigator at Washington University, approached him about building the capuchin genome.
His main role in the study was in directing the genome assembly and using this genetic blueprint to analyze different types of selection pressures that impacted the genome.
Selection pressures are environmental or social factors that make it harder for species to survive and reproduce. Yet, when a small percentage of these species do survive — possibly due to a certain gene — their populations can explode. Afterward, that particular gene becomes widespread across the new population.
“There’s a whole variety of selection pressures that are brought to bear on a species genome, and a lot of that is driven by the environment,” Warren said. “The beauty of this experiment is there are two very distinct populations of capuchins in Costa Rica.”
The study looked at two groups: one in the southern lowland evergreen rainforest where rainfall and fruit are plentiful and another in the northern lowland tropical dry forest where periodic droughts occur.
A gene that affects kidney and water maintenance in the body became a particular interest in their analysis. That could be necessary for survival for the northern population who faced a dry climate and needed to conserve water.
“We can speculate that [these genes are] associated with this adaptation,” Warren said. “We don’t know for sure, and we make that point in the paper. It’s more of a discussion about this is a possibility, and these are real signals of selection. We’re not sure exactly if we can directly correlate them with an adaptation to a dry, hot climate, but it certainly makes biological sense.”
Warren and the other researchers discovered the gene, among others, by lining up genetic codes of capuchins and other mammals to find matching sets of nucleotides. This allowed researchers to identify known and novel genes, like the ones related to brain size and longevity.
Capuchins are unique due to their long lifespans and large brain-to-body ratio. | Photo contributed by Amanda D Melin, Bond LSC.
Mike Montague, who previously worked under Warren while they were at Washington University, believes the correlation between brain size and longevity is due to genetics.
Genomes between capuchins and other animals showed differences that seemed to be tied to brain development, size and metabolizing mechanisms. Large brains require lots of fuel, so an efficient system for processing sugars would also be needed.
“Having an understanding of these genes and why they’re different in capuchins might be linked to these larger genetic pathways, [which] allow the capuchin to have this large brain,” Montague said.
As for longevity, researchers identified some genes associated with DNA damage response, metabolism, cell cycle and insulin signaling. While damage to DNA is thought to be a major contributor to aging, aging-related genes also deal with growth and development. This means researchers can’t be sure if the identified genes correlate with longevity.
While some genes found are associated with human cognition and large brain size in humans, they can’t be directly linked to human genes without further examination.
Researchers wouldn’t have been able to identify these genes and sequence the genome without a new technique developed by Joe Orkin, the study’s lead author. Orkin’s new technique, FecalFACS, isolated the DNA in capuchin feces of the animal’s intestinal cells.
Since capuchins are an endangered species, scientists can’t kill or capture them for study. Instead, they had to analyze their feces. The trouble was researchers originally had to cipher between the DNA of the food the capuchins ate and the DNA of the capuchin in feces. Orkin’s new technique allows them to sort that information easily.
“We observe this really beautiful population structure to these capuchins that live in this particular area,” Warren said. “We could not have got that… this larger number really let us get a very accurate portrayal of the population structure and how related they are to each other.”
Now that the paper has been published, the study’s next steps include expanding the sample beyond the two populations and investigating the functions of the newly discovered genes in other animals.
“There’s just a host of different questions that you could ask, now that we have this one particular genome added to the collection of other genomes for different primates,” Montague said.
When the pandemic hit, Maddie Graham’s lab life shifted focus.
The junior biomedical engineering pre-med student suddenly started to find answers by extracting RNA out of wastewater to help detect SARS-CoV-2, the virus that causes Covid-19, which reiterated how important science is in our lives.
“I don’t think medicine would be anything without research,” Graham said. “I think it’s really important to see the other side of things, understand how things have come to be and how they’ve made these medical advances. It was cool to be able to do something related to Coronavirus when the pandemic started.”
That understanding is something Graham never thought she’d seek out when she first came to Mizzou.
“I wasn’t planning on doing research because I didn’t think I would like it,” Graham said. “Originally I thought, ‘No, that’s okay I’ll focus on other things like volunteering and stuff.’”
But as she was taking classes, her friend Braxton Salcedo suggested that she work in the lab he was in.
“She has a good personality and is very intelligent,” Salcedo said. “She was a good partner in class, she pulled her weight and was a good communicator. When the professor said that he wanted to bring on more undergrads, I knew she would be a good fit.”
Graham thought it sounded interesting. She decided to apply and got the job.
Now, Graham has spent just over a year as an undergraduate researcher in the Marc Johnson lab at the Bond Life Sciences Center.
“At first I imagined that undergraduates just wash the dishes and stuff, but it was cool when he told me that you actually get to be part of the science aspect,” Graham said.
Starting out pre-pandemic, the Johnson lab focused on HIV. Graham was making new plasmids to help manipulate genes for the graduate students and Johnson to use. Now she studies SARS-CoV-2 in wastewater and community trends associated with it.
Graham’s perspective on research has certainly changed since she started. Now that she is in upper-level courses, she is starting to see an overlap between her learning and her job.
“I’m in Cell Biology, and the things I’m learning are directly related to things I am doing in the lab,” Graham said. “It’s cool when there are moments where I see why we’re doing certain things and the reasoning behind it.”
While Graham is experiencing research, she is still unsure of what she specifically wants to do once she gets to medical school.
“I have a lot of time to figure that out,” Graham said. “So somewhere down the road, after I get experience in other areas, I’ll hopefully know.”
The research is going to help her wherever she ends up.
“She has good hands-on experience here,” Salcedo said. “Just in general, she’s a good worker and she’s nice to be around too. I think camaraderie is one thing that our lab really has that I’m not sure a lot of other labs have. For the most part, all of the students in the lab get along really well.”
Covid-19 hasn’t just impacted her job, she also ended up adopting a dog at the beginning of the pandemic.
“We fostered her for a bit and then I decided to keep her,” Graham laughed. “It’s nice taking her on walks or to the dog park — except when it’s cold.”
Jay Thelen sitting amongst Liquid Chromatography-Tandem Mass Spectrometers in the lab. | photo by Becca Wolf, Bond LSC
By Becca Wolf | Bond LSC
Two decades ago Jay Thelen speculated an unknown protein anchored acetyl-CoA carboxylase (ACCase), an important enzyme complex, to the chloroplast membrane. He even published a paper about it, not knowing exactly what the membrane protein was.
Flash forward and Thelen, a professor of biochemistry and principal investigator at Bond Life Sciences Center, now knows exactly what it is, which is detailed in a recent paper in Nature Communications. And this finding could potentially lead to crops with oil in their leaves that could be harvested.
“The finding was very gratifying, it was like an itch I was finally able to scratch,” Thelen said.
The previously uncharacterized membrane protein belongs to a novel class of proteins in his lab that are now referred to as Carboxyltransferase Interactors (CTIs), based upon the screen used to identify them. Yajin Ye, a former postdoctoral scientist in his lab, discovered that once CTIs are silenced, the amount of triacylglycerol storage oil in plant leaves increased. Oil is not typically found in leaves, so this finding was surprising.
“Normally, plants accumulate oil in the seed or the mesocarp, as carbon for the germinating embryo or a reward for seed dispersal, respectively,” Thelen said. “But when Yajin knocked out the gene he found that the plant leaves began to accumulate oil at rates four-fold higher than normal.”
Building off this discovery, Thelen and his lab continued to do more experiments on ACCase. In plants, ACCase acts as the gatekeeper of fatty acid biosynthesis. And fatty acids are the principal component of the storage lipid triacylglycerol.
“The regulation of this enzyme is quite sophisticated, particularly in plants due to its modular, multi-subunit nature,” Thelen said.
They soon found that the CTI, which anchors ACCase to the envelope membrane, serves as a negative regulator, suppressing ACCase function during light. When the three CTI genes were knocked out by CRISPR, it permitted ACCase to accumulate oil in plant leaves. Thelen first showed this in the model plant Arabidopsis, but is also investigating this in other plants.
“This has potential to make an impact in crops,” Thelen said. “The long-term objective of my lab is to try to increase oil accumulation in plants. This is an interesting discovery that led us to think that maybe leaves could be an alternative location for oils. If we can raise the levels in the leaves, they could be harvested and extracted for their oils and used for industrial food and feedstock purposes instead of discarded.”
Thelen and the University of Missouri patented this discovery and licensed it to a Boston-area company Yield10 Bioscience to commercialize this idea.
Thelen plans to continue looking at ACCase to look for its limits and processes.
“We’re still focused on making basic discoveries regarding the regulation of this first step in fatty acid synthesis,” Thelen said. “There certainly are more discoveries to be made.”
Building a community through screens and limited interaction can be difficult. However, it’s no problem for Margaret Lange at Bond Life Sciences Center.
“I’ve met such wonderful people,” Lange said. “It really is true that if you surround yourself with the right kind of people who are positive, who think creatively and who ask good questions, it shows you how to model that behavior yourself. It teaches you to be better and helps you think better.”
Lange was originally part of the Donald Burke lab until she became an assistant professor of Molecular Microbiology and Immunology in the School of Medicine and established her own lab in Sept 2019, getting her start in Bond LSC lab space. Even though March 2020 brought shutdowns and restrictions, Lange still found herself in a mentoring role.
“I’ve had some mentoring experience but never as the primary investigator (P.I.) of the lab, so it’s a new experience for me,” Lange said. “I’m learning from that and learning from them and, hopefully, they’re learning some things from me as well.”
Lange understands that establishing a lab requires equipment and published papers, but also a good team.
“The reason I joined her [lab] is that women in science in a leadership role is very important and that needs to be encouraged,” said Rachna Aneja Arora, research scientist in the Lange lab. “I see her as a good leader and a good mentor. She has a very inspirational role and can be a role model for the young girls and women in science to take on the challenging role to be a P.I.”
However, Lange’s path towards science began before she even arrived at Mizzou.
Growing up in rural Missouri, Lange attended a small high school that didn’t offer many science classes beyond the traditional chemistry and anatomy classes.
“I didn’t even know at that time that you could do research in a lab,” Lange said. “I had no idea what opportunities were available.”
She did have some knowledge of microbiology since her mother was a medical technologist at the local hospital where she spent time identifying microbes that were causing infections in patients. So, Lange decided to enroll in a microbiology class once she started college. Not too long after, the professor asked Lange to help her with her research.
“If it wasn’t for her, I never would have probably tried doing research at all,” Lange said. “It’s really fun to design experiments and to answer questions. And so that was really kind of where my love for that started to show, or at least become evident to me, anyway.”
Since then, Lange has been interested in how cells can sense viruses and how that shapes immune signaling.
Humans have many receptors that can recognize different parts of viruses and can cause different immune responses based on what they’re recognizing.
“We really try to understand what is working at the level of the virus to shape those responses and how that influences how our immune system is able to fight those viruses,” Lange said.
The Lange lab is currently looking to improve the host-virus interaction regarding vaccines.
Vaccines generate a response that is specific to a certain component of a virus. However, just focusing on a single protein or nucleic acid is not enough to generate a robust and specific immune response. So, researchers like Lange are working towards improving adjuvants — immunostimulants in vaccines — to create a stronger response that helps shape antibody and T cell responses.
“Investigating what types of nucleic acid motifs can actually bind and signal through these pattern recognition receptors helps us design better adjuvants that can better shape the immune response for a specific pathogen,” Lange said. “For example, if you use a nucleic acid from the SARS coronavirus, it might shape the immune response in a specific way targeted to that specific virus, and then you hopefully get a better efficacy for your vaccine.”
For now, Lange and her team are working towards developing their lab and getting manuscripts underway.
“I really admire her for all she’s doing,” Aneja Arora said. “I think we will work harder to get things moving forward. So, I just wish her all the best and wish her good luck setting up a very established lab.”
Metabolite screening looks to better understand cancer
Research scientist Rajarshi Ghosh in the Lloyd W. Sumner lab loads samples into the Nuclear Magnetic Resonance (MNR) spectrometer for analysis. | Photo by Lauren Hines, Bond LSC.
By Lauren Hines | Bond LSC
Doctors take blood or urine samples to see what’s going on in the body of a patient, and that’s not all that different from what metabolomics scientists do when looking at metabolites.
“[The doctor] may profile 20 or 30 compounds to try to understand what’s going on with your physical health and well-being,” said Lloyd W. Sumner, director of the MU Metabolomics Center. “Well, that’s what we do but on a larger scale. Instead of analyzing 20 or 30, we’re analyzing hundreds to thousands of individual chemicals, specifically metabolites, that are in your body. This provides a high-resolution biochemical phenotype for our subjects.”
Even though metabolites are relatively small molecules compared to DNA and proteins, they play a big role in every organism.
Metabolites serve as energy sources and building blocks that are the end products of our cellular processes. These molecules can tell researchers in the Metabolomics Center at Bond Life Sciences Center a lot about what goes on in the bodies of plants and animals and offers potentially great opportunities in precision health.
One specific example happened in July 2020 when the Metabolomics Center and the Rat Resource and Research Center highlighted what looking at metabolites can do in a new publication.
“We were able to show from the metabolic profiles that we could predict [colon] cancer or the tumor load [in rats] well in advance,” Sumner said. “Thus, metabolomics is a very powerful diagnostic and prognostic tool that we were just beginning to realize, and we would ultimately like to move metabolomics into the clinical medical arena as well and use it in personalized medicine.”
However, researchers were asking a different question at first.
“We’ve always thought about the gut microbiome,” said James Amos-Landgraf, associate professor of veterinary pathobiology at the Rat Resource Center. “What is the mechanism behind [the bacteria in the gut] influencing cancer development? And one of the possibilities certainly could be the metabolites that are being produced by those bacteria.”
Researchers took two genetically identical sets of rats, which were genetically susceptible to cancer, and introduced different microbiomes in each group. Then, they analyzed the metabolites in the rat feces and blood.
“What was interesting to us was that at one month of age, there were metabolites that could predict at four months whether or not they had more tumors or less tumors,” Amos-Landgraf said. “That was somewhat independent of the microbiome, so it certainly correlated slightly with what microbiome was there, but it was more about what those bacteria were actually producing.”
Now, researchers have to identify the metabolites in the profile to better understand the biochemistry and mechanism of cancer proliferation. However, only a few percent of metabolites have been identified to date. The Metabolomics Center continuous to expand its efforts in metabolite identification by measuring the size, charge and structure of these molecules.
“Metabolomics is really crucial to understanding the role of the gut microbiome,” Amos-Landgraf said. “Understanding both what the gut is producing and how our body responds to that is going to be crucial. So, moving forward that’s the direction we’re taking.”
According to the Centers for Disease Control and Prevention, cases of colon cancer have decreased in older populations due to screenings. Those screenings allow doctors to remove benign tumors before they spread. Additional diagnostics can potentially further decrease cases.
Researchers like Amos-Landgraf and Sumner see the metabolites that were present in the less susceptible animals as acting as a potential preventative. While very long down the road, the metabolites could be used as a screening technique to predict cancer in people.
“Cancer is kind of a flagship focal area for me because it’s a very metabolically dysregulated disease,” Sumner said. “Trying to understand that process will hopefully lead to new information and better health overall.”
It’s not a straight line between basic research and Silicon Valley, but Shuai Zeng made the dots connect.
Last summer, Zeng, a Ph.D. candidate in computer science, had an internship at Google headquarters in Mountain View City, California, where he worked on an applied research team. There, he helped design and develop a state-of-the-art deep learning model about video recommendations for Google Ads and YouTube.
Deep learning mimics the workings of the human brain in processing data through artificial intelligence (AI). It is used in detecting objects, recognizing speech, translating languages, and making decisions. Examples of deep learning would be Amazon’s Alexa and the navigation abilities of self-driving cars, like Tesla.
“At Google, I felt like I was working at a college like Mizzou,” Zeng said. “Working there required me to learn a lot of new things in a very short time. I learned not only coding skills, but also creative, analytical, and research skills.”
Zeng currently works in the University of Missouri School of Medicine and Bond Life Sciences Center under Dr. Trupti Joshi’s guidance. He finds it beneficial to build a bridge between his knowledge of computer science with the likes of medicine and plant biology.
“I currently work on the infrastructure for collecting and integrating multiomics data on soybean, maize, Arabdopsis, human, mouse, and many other organisms,” Zeng said. “The website provides a lot of interesting tools that allows the researchers to see, analyze, and store their data online. I can do the data analysis for them so they can go to the website and see the results from huge datasets and easily extract information that they need.”
Zeng also credits his time and experience at Bond LSC to helping him get the Google internship last summer.
“I work on a lot of different projects here, which is good because working with Google requires having a strong background,” Zeng said. “If I only work on the computer science part, it is not good enough because you need to learn a lot of other things as well.”
Zeng even enjoys combining computer science with biology, despite the difficulty.
“Fortunately, there are a lot of very good students here at Mizzou, so I don’t need to learn biology on my own. I just ask them some questions about it and then I can get to work,” Zeng said.
His advisor, Trupti Joshi, appreciates his willingness.
“He’s a very dedicated and motivated student,” Joshi said. “He does a fantastic job of translating and understanding the deep purpose of what the data issues are. He’s been one of our really crucial contributors in the lab.”
Zeng enjoys the environment at Bond LSC because of its similarities to Google. At Bond LSC, he works in the Joshi lab, where he aids in data analysis. One of the main things he works on is the Soybean Knowledge Base (SoyKB) and Knowledge Base Commons (KBCommons) frameworks.
“He really contributes to new developments, new methodology implementations, and developing and maintaining some of these crucial frameworks that we use for collaboration with faculty here and also outside,” Joshi said. “He’s going to have a fantastic career trajectory with all the experience he has gained from these research projects and internships.”
Zeng hopes that career involves going back to a large company like Google after he graduates.
“In the next five years, I would love to get a full-time job as a research scientist at Google or Facebook and be learning as many new things as possible,” Zeng said.
Until then, he will continue learning as much as he can in labs here at Mizzou.
By Lauren Hines | Bond LSC
