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CALS Weekly

CALS Researchers Return to the Bench and Field

A group of students in a corn field as the sun sets. (From Summer 2019)
Nicole Choquette, a Ph.D. student in the Department of Crop and Soil Science, and her teammates work in the field during the summer of 2019. As CALS researchers are returning to the field and the lab bench, they are maintaining strict safety guidelines.

Researchers across the College of Agriculture and Life Sciences are returning to the lab bench and test field.

The second phase of NC State’s Research Restart process began on June 8. This allows for increased occupancy of laboratory facilities across campus, while still requiring enough space for researchers to follow social distancing guidelines.

During Phase I, which began May 18, the university’s goal was to slowly work up to a 35 percent occupancy of laboratory facilities. On a case-by-case basis, the university reviewed requests to allow researchers — graduate students, postdoctoral fellows, research technicians and faculty — to return to a laboratory room to conduct critical experiments one or two at a time.

The Alonso-Stepanova lab, jointly run by Jose Alonso, William Neal Reynolds professor of plant and microbial biology, and Anna Stepanova, an associate professor in the same department, received permission for three of its eight full-time researchers to return to the lab — one at a time.

“The decision who got to come back first was made by the lab collaboratively, taking into account both the urgency of the experiments and how comfortable these employees felt returning to work,” Stepanova said. “Some of our lab members have young kids at home who need supervision, or elderly parents who are in a high-risk group for COVID-19, making it necessary for those employees to continue working from home.”

During the pandemic, a number of labs were granted limited exceptions to keep living organisms alive — from genome-edited plant cells to cattle for research on the research stations and field labs. The Research Restart process is building on those early exceptions so that important research can resume safely.

“I think NC State is making decisions based on science and data,” said Javier Brumos, a research scholar in the Alonso-Stepanova lab. “The University is rightly being cautious to minimize the impact of COVID-19 on the Pack. The situation generated by the pandemic has had a clear negative impact in our research, but I totally understand and support NC State policies.”

Here’s how three scientists are making the transition back to hands-on research safely.

Wusheng Liu, Horticultural Science

The members of the Liu Lab around a large table with a white tablecloth during a celebratory meal.
The members of the Liu Lab around a large table with a white tablecloth during a celebratory meal. Front: Sihui Ni; left side from front to back: Meghan Roche, Paul Kosentka, James Duduit, Via Abiera, Debao Huang; Right side from front to back: Morgan Miller, Wusheng Liu, Alice Liu, Xianlian Chen, Liwei Gao. (Photo from Oct 2019)

Wusheng Liu, an assistant professor in the Department of Horticultural Science, studies new methods to edit plant genomes in a non-GMO manner, and has irreplaceable genome-edited plant cells and plants.

“In March, we were approved to keep my transgenic calli and plants — tomato, camelina and lettuce — and sweetpotato cell lines growing,” Liu said. “If we lost them, I would have lost everything. I have two postdocs who took turns going into the lab every other day to maintain the plants and the cell lines. One of them went in to the lab one day and then the other would go in two days later.”

During Phase I of the Research Restart process, in addition to maintaining the transgenic plants and cell lines, Liu’s lab was given approval to harvest fruit from over 100 different breeding lines of purple tomatoes that were planted in February. The project, which is a collaboration with Penelope Perkins-Veazie, a professor of Horticultural Science based in Kannapolis, aims to investigate the underlying mechanisms of anthocyanin biosynthesis, a plant nutrient more commonly found in blueberries.

Liu’s team is harvesting the purple tomatoes, to crush them and store them in an ultra-cold freezer for later analysis.

While not keeping plants alive or conducting critical experiments, Liu’s lab has been writing papers and sections of their graduate dissertations.

“Most of the people are focused on writing up whatever they can write, even if it’s just maybe part of their dissertation or the methods section of a paper,” Liu said. “I don’t want to push people too much. Everybody’s under stress. But by writing one or two pages each day and then sending it to me to edit, they will feel like they were productive several months later.”

Javier Brumos, Plant and Microbial Biology

Two researchers in chamber holding a tray of tomato seedlings of different heights.
NC State’s Anna Stepanova and Javier Brumos are studying translational activity involved in tomato ripening. (Photo from 2018)

Javier Brumos is a research scholar in the Alonso-Stepanova lab who studies auxin, a critical plant growth hormone, and the enzymes involved in making it.

Brumos was granted an exemption to maintain his irreplaceable tomato transgenic lines both in the laboratory and in the Method Road greenhouse prior to Phase I. During Phase I, three other members of the Alonso-Stepanova group were allowed to return one at a time to the laboratory in Thomas Hall to work on critical experiments.

Instead, he has been analyzing data from past years that he hadn’t had time to look at before, and catching up with the latest scientific literature. Additionally, he has taken several free online courses, including a course on writing in the sciences offered by Stanford University.

“I have taken several courses to improve my writing skills and expand my expertise in areas like plant biology and genetics,” Brumos said. “The time we are ‘forced’ to spend at home combined with the huge offer of free-online courses provides an unbeatable opportunity for personal career growth and development.”

Brumos’ colleagues have also been taking courses, analyzing data, writing papers, organizing and digitizing lab notes, catching up on scientific literature, reviewing papers, attending online seminars and planning future experiments.

Brumos thinks that the explosion of online seminars has been the real silver lining of the COVID-19 pandemic.

“This new normal has brought some positive outcomes such as online seminars, meetings, and conferences are becoming more accessible,” Brumos said. “No matter who you are or where you are — as long as you have an internet connection — state-of-the-art research and knowledge is at your fingertips. Online seminars democratize the availability of knowledge regardless of one’s location. I hope this situation will make the scientific community re-think the way we organize meetings and conferences in the future.”

Nicole Choquette, Crop and Soil Science

Woman smiling in field of corn.
Nicole Choquette studies how to adapt tropical lines of maize to North Carolina. (Photo from 2019)

Partly due to the greater ability to maintain social distancing guidelines while outside, more off-campus research projects were approved prior to the University entering the second phase of the Research Restart process.

One of these approved off-campus research projects is Nicole Choquette’s thesis research. Her project is focused on adapting tropical lines of maize to North Carolina, using genomic selection to speed up the process.

Choquette is a Ph.D. student in the Department of Crop and Soil Science who just completed her first year. She is co-advised by Jim Holland, a U.S. Department of Agriculture-Agricultural Research Service plant breeder, and Rubén Rellán Álvarez, an assistant professor in the Department of Molecular and Structural Biology.

Holland was able to get an off-campus research exemption so that his team could plant critical varieties — including the lines Choquette needs for her thesis research — during the corn planting time.

To plant their varieties on the research stations, Choquette and her teammates drove with only one person in each car instead of carpooling. While working, they stayed well over six feet away from one another — typically one person per plot — and wore proper personal protective equipment, including face masks.

“Last year we had a big group of people and we all carpooled together and this year it’s more individual,” Choquette said. “For example, today I went out to the field because I had to go thin my plots. Last year, we had a lot more planted and we’d do stuff together. We also don’t have any undergraduate researchers this summer.”

When not out in the field, Choquette has been analyzing data from a prior project and preparing for her oral exam. The oral exam is a milestone every Ph.D. student must complete. It involves being questioned by a handful of departmental faculty members to judge the breadth and depth of the student’s knowledge and understanding of their field of specialization. Choquette’s oral exam took place over Zoom, instead of the traditional in-person trial.

“Being in grad school during a pandemic is something I won’t ever forget,” Choquette said. “In March, during the stay-at-home orders, it was kind of tough, especially as someone who loves being in the lab and being surrounded by my labmates. But I think everybody did the best they could to transition. Jim Holland really cares about our safety and I feel like NC State is doing its best to keep everyone safe.”

CALS is working together to tackle the challenges of COVID-19.