Stacey Lab and Missouri Life Sciences Week 2018.

Joining in the energetic Missouri Life Sciences week 2018, Stacey Lab members had a wonderful time participating and exchanging ideas.

Ph.D. student, Beverly J. Agtuca shared her research on applying new mass-spectrometry methods to understand the rhizobial-soybean symbiosis.  Beverly was one of only 6 students in the physiology category who were recognized at the awards ceremony for her work.

One of our youngest scientists, undergraduate Sterling Evans presented a very nice poster focused on improving methods for CRISPR/CAS9 editing of soybean using virus-based vectors. Missing is a similar picture of the poster by undergraduate Miki Hodel, who conducted related research focused on using different promoters to increase CRISPR/CAS9 editing efficiency.

A visiting Ph.D. student from Brazil, Marina Cotta, discusses her poster with Ph.D. student Cuong Nguyen. Marina is another example of our very productive and continuing collaboration with the University of Parana in Brazil focused on understanding the mechanisms by which plant growth promoting bacteria interact with plants.

Cuong Nguyen and the rest of our laboratory congratulation Beverly Agtuca on her award for the outstanding poster.

Thank you to all who came to enjoy visiting our posters and to support Missouri Life Sciences Week. See you next year!

A bitter sweet moment saying goodbye to Shakhawat as he leaves the lab for a nice job at Pivot Bio, Inc. in California. We will miss him but wish he great success in the future.

Dr. Gary Stacey elected as a Fellow of the St. Louis Academy of Science

“Since its inception, the Academy has promoted the recognition of the impressive scientists of St. Louis. This tradition continues with the 24th Annual Outstanding St. Louis Scientists Awards. Each award-winner represents an extraordinary caliber of expertise”.

“The Fellows Award recognizes a distinguished individual for outstanding achievement in science”.

Gary Stacey, Ph.D.
Curators’ Distinguished Professor
University of Missouri, Columbia

Dr. Stacey is a Curators’ Distinguished Professor at the University of Missouri-Columbia. He has consistently been among the world leaders in the study of biological nitrogen fixation, which is of global agricultural importance. He has been instrumental in the development of genomic resources for the study of soybean. He has 13 patents, two of which support the Novozymes product OptimizeTM. He was elected a Fellow in the American Academy of Microbiology and Fellow of the American Society for Plant Biology. Stacey’s main research interest lies in the mutually beneficial interaction between nitrogen-fixing bacteria and legumes, particularly soybeans. Soybean with its high protein content and nutritious oils is a crop of paramount importance to Missouri, the US and the world. Soybean plants are able to harbor bacteria in their roots that take gaseous nitrogen from the air and convert it into nitrogen-containing compounds the host plants can utilize. This natural fertilization translates into lower fertilizer requirements, with direct economical and ecological benefits in agriculture. In addition, Stacey’s research program creatively combines research with soybean and the model plant Arabidopsis, which is not able to accommodate bacterial nitrogen fixation, to tease apart the perception of microbes as friends or foes. This combination and the vast array of genetic, molecular, and biochemical approaches and their current -omics versions that Dr. Stacey employs to investigate fundamental questions in plant biology creates an outstanding research environment for young and ambitious scientists.

For more information: https://www.academyofsciencestl.org/awards/

Congratulation Dr. Gary Stacey !!!

Adama , a PhD student from the Stacey lab, participated in a fundraising for cancer research on November 23rd, 2017 and he won a 5km run competition in his age group. This event is organized by Boone hospital, annually.

Congratulation Adama!!!

An Unexpected Path – Plant sciences student strives to obtain an education for the greater good

Written by Jacob Shipley · October 13, 2017

Link to original story with photos

When Adama Tukuli, doctoral student in the Division of Plant Sciences, was growing up in Metahara, Ethiopia, attending school was not commonplace.

“They love their kids and do everything they can for us, but they just don’t understand education is something we need,” Tukuli said.

He was still young when he met a man who had attended school and became an engineer. Tukuli viewed him as a role model and grew determined to make education a priority.

In a primarily agricultural economy, children are usually required to stay home and assist with the farm. This meant that Tukuli had to convince his family to let him leave the cattle so he could attend school during the day. It did not help that school was 20 kilometers (12 miles) away.

Tukuli’s parents allowed him to attend, but the work on the farm did not disappear. He would run to school early in the morning, attend class, run home and then work late nights back at home.

Years and many unexpected events later, an education is still a top priority for Tukuli.

Lighting a spark

It was in ninth grade civics class when Tukuli first heard of impending agricultural problems associated with the global population growth. Growing up on a farm, he was surprised to learn that it may soon be a struggle to feed everyone on the planet. Tukuli said this was the event that lit his lasting passion for plant sciences.

He began his college career at Jimma University in Jimma, Ethiopia, and quickly became involved in the student association working with the community, raising awareness for HIV and more. As a senior, he became president of the organization.

During the summer following Tukuli’s junior year, he received a horticulture internship in Addis Ababa, the capital of Ethiopia. While working with local rose growers, he discovered that their main cost was paying for coco peat, a medium to germinate the roses. This piqued his interest and resulted in further research during his senior year. Tukuli noticed that fermented coffee pulp looked very similar to the coco peat and thought it was worth trying. The results were promising.

“That byproduct (coffee pulp) that no one was using, a pile the size of this building, now became usable,” Tukuli said.

His invention germinated the roses even better than the coco peat. Tukuli and the student association freely shared this newfound information with the farmers, resulting in a quick friendship.

“They loved me and I loved them,” Tukuli said.

After graduating top-three in his class, Tukuli temporarily stayed at the university as an employee, but soon applied for a scholarship, and ultimately left to pursue a master’s degree, at Leibniz University of Hanover in Germany.

During summer break after his first year at the university, he reconnected with an old friend, Fatuma Hullo. Tukuli and Hullo had known each other since high school, but now sensed something more than a friendship. The two married prior to Tukuli heading back to school.

Unquenchable flame

During the second year of his studies, news broke out from Ethiopia. The student organization that Tukuli had been a part of was under attack from the government. The farmers that they had been working with were protesting against the government and the student association was under suspicion of colluding with them.

Tukuli said the organization had simply been helping the farmers grow roses and teaching them about the importance of education.

“To the best of my knowledge, we didn’t do anything bad,” Tukuli said. “All of my friends, the student association members, they got jailed – some of them killed.”

Knowing he was unable to return to Ethiopia, Tukuli recalls telling one of his professors, “I’m not even able to continue my education. I just want to get a stable life first.”

Tukuli fled to the United States in search of asylum and stayed with a friend living in St. Louis, Missouri. He was granted asylum in November of 2011. Tukuli’s wife was able to leave Ethiopia and join him in the United States as part of the “family reunion” program for asylum recipients.

Once approved to work, he found a job as a cashier and soon after as a lab technician at Monsanto in Chesterfield, Missouri, where he worked for the next two years.

In 2015, Tukuli had resided in the United States for five years without a criminal record, making him eligible to apply for citizenship. Through studying for the required test, he learned about the country’s history and became intrigued.

“When I was applying for my citizenship I came to learn a lot,” Tukuli said. “This country saved my life so I decided to serve.”

Tukuli enlisted with the Army Reserve and was stationed with a unit in St. Louis. He will remain enlisted until 2023.

Fanning the fire

Despite the detour, education was never far from Tukuli’s mind.

“That was a transition time for me to establish myself,” he said. “My plan was still to become a student.”

Tukuli took a leap of faith and left the attractive pay at Monsanto to come to Columbia with dreams of getting a doctorate. Henry Nguyen, Curators’ Professor of Plant Sciences, found him a spot as a lab technician working in his molecular genetics and soybean genomics laboratory. Tukuli used the employee tuition assistance program to work on graduate classes, taking one class per semester to avoid student loans.

James Schoelz, professor in the Division of Plant Sciences, taught one of Tukuli’s classes and the two kept in touch. They eventually found a way to get Tukuli back in school full-time. With Schoelz’s help, Tukuli applied for a position working as a lab technician in the Stacey Lab and for a fellowship to fund his education. In August, he began his first semester as a full-time Ph.D. student. Because of previous coursework, Tukuli is able to focus the majority of his time and effort on research.

“It’s a good program – I like it,” Tukuli said. “Most of the professors are really helpful. They are nice and have good advice. The professors work as a team to produce tomorrow’s leaders in science. I recommend this program to anybody who wants to study plant science.”

Minviluz (Bing) Stacey, assistant research professor in the Division of Plant Sciences, recalls getting the call asking to find Tukuli a spot in her lab as a technician.

“I really didn’t have that much money, but I said ‘I can talk to him,’” Stacey said. “He really wanted a Ph.D. and I wanted to give him the chance.”

Stacey was impressed with his dedication to taking classes and pursing an education amidst his difficulties. Ultimately, she was able to find him a spot.

“He is very positive and very kind,” Stacey said. “He’s always willing to help.”

In addition to cooking up Ethiopian cuisine for the lab parties, Tukuli joined other students and visited Stacey’s home while she was ill. He said he is thankful for the role that both Gary and Bing Stacey have played in helping him in the transition to become a full time Ph.D. student.

Since ninth grade civics class, much has changed for Tukuli. In addition to playing the role of lab technician and student, he has the title “dad” to Bilisummaa (4) and Nimoona (2). Despite his growing family in the United States, he is unable to visit his family back home so long as the current government is in power.

While not running to and from school anymore, he still finds time to train for his health and for the Army. After returning from basic training, he overheard about a Columbia staple, the Turkey Trax, a Thanksgiving Day race. He entered and won his age division. Tukuli is also a member of the graduate professional council for the Department of Plant Sciences Graduate Student Association.

The root of Tukuli’s drive remains steadfast.

“When I say I study plant sciences, it’s personal to me. I’ve been through a lot in Africa and I know people are suffering from shortage of food. Now, I am living in the developed world with my family where people want quality food, so food quantity and quality is personal to me.” Tukuli said. “I just want to work on plants and cure the quantity and quality problem. I think it’s the right thing to do and I believe in that and I want to do that.”

Beverly, a PhD student in the Stacey lab, was select for the American Society of Plant Biologists Scholars Program sponsored by CONVIRON. Congratulations Beverly!

Click here to see the program details

Sterling Evans #IAmScience

By Allison Scott | Bond LSC – See the Original Story Here

“#IAmScience because I want to focus my research on problems that exist in agriculture in undeveloped and third world countries.”

Sterling Evans’mind wasn’t focused on research when he started college, but that would soon change.

The sophomore plant sciences major uncovered his interest thanks to Freshman Research in Plant Sciences (FRIPS) — a program dedicated to introducing research to freshman students from plant-related degree programs.

“I was interested in plant sciences-related fields when I started here, but I had no intention of getting involved in undergraduate research,” Evans said. “Being selected for FRIPS was instrumental in getting me involved with research.”

Along with a handful of students selected for FRIPS each year, Evans got to interact with various professors and mentors around campus on a weekly basis. Because of that exposure, Evans found a place in the lab of Bond Life Sciences Center’s Gary Stacey.

After a year working in Stacey’s lab, Evans just joined a new project that aims to improve the nutritional value of soybeans.

“They’re used as a main source of protein for a lot of countries, so improving their nutritional content would have a huge impact,” Evans said.

The team is applies CRISPR, a gene-editing tool, to model plants called Arabidopsis as a first step.

“We are working on Arabidopsis right now as a proof of concept, because it can be done in a relatively short period of time, before investing as much as a two additional years in soybeans,” Evans said.

While he only spends 15 hours in the lab each week, Evans noticed the lab’s impact on his approach to academics in other ways.

“Research gives me more motivation to think about how to apply information I’ve learned in class to work in the lab,” Evans said. “It has made me more analytical in classes because I have more of a desire to understand things.”

Evans plans to earn a Ph.D. in a plant sciences field and wants to continue research in his career. He’s most interested in helping ensure small communities throughout the world have enough to eat, and he hopes to contribute by studying orphan crops.

“I think they’re cool because they’re really important to small people groups. No one studies them because they aren’t a big deal in the United States or other countries,” Evans said. “If we work on them we won’t have a huge impact on hundreds of millions of people, but we will have a huge impact on small communities.”

That impact all started in a lab. Had he not stepped out of his comfort zone he might never have discovered this path, and he highly encourages other students to give research a chance.

“There are labs for almost everything and there’s an area for everyone,” Evans said. “I didn’t know I wanted to do research until I did it.”

ASPB Conviron Scholars Program

Open to exceptional undergraduate and graduate students studying plant biology, the ASPB Conviron Scholars program delivers an experience intended to serve as a foundation for a career in plant science. Applications welcome from any country.  Students who apply to the program must be in good academic standing (verified by their Pl or department head) and must demonstrate a commitment to plant science. For the 2017 program, a total of 20 students will be chosen to participate in the ASPB Conviron Scholars program.

Drowning in Data

By Emily Kummerfeld | Bond LSC (Original Story)

New web-based framework helps scientists analyze and integrate data

Large-scale data analysis on computers is not exactly what comes to mind when thinking about biological research.

But these days, the potential benefit of work done in the lab or the field depends on them. That’s because often research doesn’t focus on a single biological process, but must be viewed within the context of other processes.

Known as multi-omics, this particular field of study seeks to draw a clearer picture of dynamic biological interactions from gigantic amounts of data. But, how exactly can scientists suitably weave multiple streams of information together, especially considering technology limits and other biological variables?

Trupti Joshi and her team are seeking to find a solution to that problem.

Joshi, as part of the Interdisciplinary Plant Group faculty, works on translational bioinformatics to develop a web-based framework that can analyze large multi-omics data sets, appropriately entitled “Knowledge Base Commons” or KBCommons for short. She describes KBCommons as “a universal, comprehensive web resource for studying everything from genomics data including gene and protein expression, all the way to metabolites and phenotypes.”

Her work began about eight years ago with soybeans. Dubbed the Soybean Knowledge Base (SoyKB), her team had developed a lot of their own data analysis tools for soybean research, but they realized the same tools could help research of other organisms. From there sprouted the Knowledge Base Commons, intended for looking at plants, animals, crops or disease datasets without the need to “reinvent the wheel” each time.

Soybean plants used in research that utilizes Soy KB web-based network. | Emily Kummerfeld, Bond LSC

“Our main focus has been in enabling translational genomics research and applications from a biological user’s perspective, and so our development has been providing graphic visualization tools,” Joshi said.

Those tools provide an array of colorful graphics from basic bar graphs to assorted colored pie charts to help the researcher better analyze the data once data has been added to the KBCommons.

Colorful graphs and comparisons let many researchers look past the lines of text and tables full of numbers that represent genes, plant traits or other experimental results, and making the interpretation of data much easier and efficient.

One particular tool allows the researcher to look at the differential genes of four different comparisons or samples at the same time. Differential genes are the genes in a cell responding differently between different experimental conditions. For example, a blood cell and a skin cell both have the same DNA, however, some genes are not expressed in the blood cell that is expressed in the skin cell. With this KBCommons tool, a researcher can examine genes to see “what are the common ones, what are the unique ones to that, and at the same time look at the list of the genes and their functions directly on the website, without having to really go and pull these from different websites or be working with Excel sheets,” Joshi explained.

She envisions KBCommons as a tool to enable translational research as well. Users will be able to compare crops, such as legumes and maize for food security studies, or link research between veterinary medicine and human clinical studies for better therapies.

Intended for a wide range of users, Joshi is keenly aware of its potential users right here at MU.

One current user of the Soybean Knowledge Base (SoyKB) system is Gary Stacey, whose lab at Bond Life Sciences Center studies soybean genomics and to date has been the longest user of the SoyKB resource. Like many researchers, Stacey explained the need for a program like SoyKB that can process enormous amounts of data.

“The reason it’s called “Knowledge Base” is the idea that we’re putting information in, and what we hope to get out is knowledge. Because information is different than knowledge,” he said, “we don’t just want to collect stamps, we want to be able to actually make some sense out of it…By having a place to store the data, and then, more importantly, have a place to analyze it and integrate it, it allows us to ask better questions.”

This is essential, given that one soybean genome is 1.15 GB in size, and one thousand soybean genome sequences could generate 30 to 50 TB of raw sequencing data and tens of millions of genomic variations (SNPs).

But such numbers are modest compared to the program’s true capabilities.

“The KBCommons system is so powerful that it can allow you to run thousands of genomes at the same time using our XSEDE gateway allocations,” Joshi said. “This whole scalability is a unique feature of KBCommons, which a lot of databases do not provide, and we are happy we have been able to bring that to our MU Faculty collaborators on these projects, so that they can really utilize the remote high-performance computing (HPC), cloud storage and new evolving techniques in the field.”

KB Commons is a new web-based network for biological data analysis and integration developed by students. | Emily Kummerfeld, Bond LSC

Mass data capability and colorful graphs aside, her favorite part is who exactly is designing the program.

“What I like most about KBCommons is that it serves as a training and development ground and is developed by students, undergraduate and graduate students from computer science and our MUII informatics program.”

KBCommons is still under development, but publication and access for all users are planned for the end of this year or early 2018. Users will not only be able to view public data sets but add their own private data sets and establish collaborative groups to share data.

Dr. Trupti Joshi is an Assistant Professor and faculty in the Department of Health Management Informatics, the Director for Translational Bioinformatics with the School of Medicine, and Core Faculty of the MU Informatics Institute and Department of Computer Science and the Interdisciplinary Plant Group.

Beverly Agtuca #I Am Science

Original Story by Roger Meissen

Beverly Agtuca was born in New York, but has family in the Philippines, a country that struggles with malnutrition and undernourishment. Her overall goal for her research is to help countries that struggle with undernourishment by increasing the agricultural productivity in those countries.

“When I was little, I went on summer vacation to visit my family, which included my grandmother in the Philippines,” she said. “Everyday my grandmother wanted me to go out to the rice fields from 5 a.m. to 10 p.m. with the other children to get rice for our meals. That was not an easy task and that moment changed my life. That’s when I decided that I wanted to be a plant scientist.”

Agtuca graduated in 2014 with honors in Biotechnology and a minor of Microscopy from the State University of New York College of Environmental Science and Forestry (SUNY ESF) in Syracuse, NY. She’s currently a Ph.D. candidate in plant breeding, genetics, and genomics at MU. She chose to come to Bond LSC because of the community and Dr. Stacey, her supervisor and mentor.

“If you ever need help, there’s always help here,” she said. “Everyone at Bond LSC is so kind, including the staff. I love to make small talk with the custodians and they are always supporting me and say I should never give up when I have a bad day.”

Ever since coming to MU in 2014, Agtuca has been keeping busy. In June, she received a travel award to go to the American Society of Plant Biologists (ASPB) in Hawaii. The International Society for Molecular Plant-Microbe Interactions (IS-MPMI) also awarded her a travel award to attend the 2016 meeting in Portland, Oregon, where she gave an oral and poster presentation. She also has two original research publications under her belt and is currently working in Dr. Gary Stacey’s lab at Bond LSC.

The research for her dissertation is focused on the relationship between rhizobia and soybeans. She collaborates with scientists at George Washington University (GWU) in Washington, D.C. and the Pacific Northwest National Laboratory (PNNL) in Richland, Washington to enhance the capabilities of the 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T FTICR) through application of laser ablation – electrospray ionization mass spectrometry (LAESI-MS) technology that can analyze the contents of single plant cells. This 21T FTICR machine was recently installed at PNNL and represents one of only two such machines in the world.

This is revolutionary because few people do single cell analysis. Usually, scientists deal with the law of averages, which dilutes the final measurements. But this technology gives an in-depth glimpse into a single cell so scientists can obtain a more comprehensive bigger picture.

“After we finish building this technology, we want to spread the technique to different research groups so they can answer these research questions on their own,” said Agtuca. “It can help people outside of plant sciences too, and hopefully will help with cancer treatment and disease prevention.”