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Handling Large-Scale Plant Research Projects

Ivone Torres-Jerez shares her experiences, from growing up in Mexico to finding her professional home at Noble Research Institute, and offers tips to researchers on how to manage large-scale projects.

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As a child in Tampico, Mexico, Ivone Torres-Jerez watched with fascination the laboratory scientists at the clinic where her mother took her for her annual wellness checkup. Torres-Jerez thought they were doing important work and someday she wanted to do the same.

Laying the Foundation

After earning bachelor’s and master’s degrees in biology, Torres-Jerez, currently a senior research associate and laboratory manager at Noble Research Institute, joined Secretaria de Agriciltura y Recursos Hidraulicos, a prestigious agricultural research center in Tamaulipas, Mexico, as its first lab researcher. There she met her husband, also a scientist.

The couple moved to Mexico City where, at the International Maize and Wheat Improvement Center, Torres-Jerez established a genetic linkage map for maize. When her husband received an offer to complete a doctoral degree in the United States, the pair relocated to Tucson, Arizona, where she continued her maize genetics research as a lab manager at the University of Arizona. She also worked with whitefly-transmitted geminiviruses, helping to identify many DNA viruses in tobacco, tomato, pepper, cucumber and other plants.

The Turning Point

Then came another professional turning point.

Torres-Jerez’s husband was offered a postdoctoral position at the Noble Research Institute. When he returned from his interview, he was so excited and impressed with the facilities and dynamics that his wife thought she, too, would like to work there and, as she says, “be a part of that circle.”

She was right. Now in her 22nd year at Noble, Torres-Jerez manages the lab of chief scientific officer Michael Udvardi, Ph.D. Her responsibilities include coordinating and participating in research projects, coordinating external collaborations, providing technical advice and support and generally overseeing lab activities.

While at Noble, she has worked with plant species including Medicago, Lotus, cowpea, alfalfa, peanut and Arabidopsis.

Below she shares her experiences and offers advice to other researchers who manage large-scale projects.

Ivone Torres-Jerez extracts DNA from wheat samples.Ivone Torres-Jerez, senior research associate, extracts DNA from wheat samples as part of ongoing research at Noble Research Institute to identify naturally occurring helper bacteria that assist the plant in acquiring nitrogen more readily from its environment.

What are the challenges of managing a large lab?

One important aspect of being a lab manager is to be able to plan ahead. This helps ensure I am on top of everyday activities — making sure the lab runs smoothly and we meet our research goals as a team.

My responsibilities include coordinating and performing projects with postdocs, students and other visitors, providing technical advice and support, and overseeing lab activities in general. In parallel to this, I coordinate external collaborations/projects/requests to make sure they are completed in a timely manner. I feel supported, trusted and also appreciated by my PI, and that makes the work go beyond just a task list.

What do you enjoy most about your job?

I like working as part of a team. When I can be part of a group of smart people who get together and feed off of each other’s ideas, I feel that my knowledge, and consequently interest, rises.

What is the one skill you acquired here that you are most proud of?

I learned how to work with legumes. I was and still am fascinated by the process of nodulation, which is how legumes acquire nitrogen from air when helped by soil bacteria. This allows the plant to not need added fertilizers, which is an important component of regenerative agriculture.

What was the most surprising thing you found out about the job when you started working?

After working at a university as a lab manager, I was surprised that here we didn’t just work with our own group but coordinate with multiple groups within the organization. This internal collaborative environment helps us better work together to find solutions to unexpected situations and produce better outcomes that add to the science community’s knowledge and ultimately benefit farmers and ranchers.

Ivone Torres-Jerez sits at her lab bench at Noble Research Institute.Ivone Torres-Jerez sits at her lab bench at Noble Research Institute, where she currently manages the laboratory of Michael Udvardi, Ph.D., the organization’s chief scientific officer.

What advice do you have for someone thinking about applying for a lab manager position?

Besides having the required technical skills, be aware of your own soft skills especially to multitask and be a team player. Being neutral, open-minded, honest, responsible, hard-working and going beyond what is expected also helps.

What resource development projects have you participated in?

I constructed the Medicago truncatula EST libraries in the early 2000s and was responsible for probably 75% of the generated libraries. I was instrumental in developing the Medicago and Lotus gene atlases and the RNAseq atlas on the MtSSPdb because I was the main person involved in planning and setup, processing the samples, and also training new postdocs to work with the legumes. These widely used resources are already publicly available.

What factors do you need to consider before starting a large-scale project?

First of all I make a scheme of the experiment and plan ahead on paper. I take into account how large the scale of the experiment is then I calculate how many people, material, space — plant growth chamber or greenhouse, plant material etc. — that the experiment will need. However, the biggest task I see is coordinating among the researchers on the goals of the project so that everyone has a global idea of the main objective. Some parts of the project require delegating tasks to individuals, after which we get back together, verify what we found out and decide what we need to do next.

How do you record the outcomes?

On a personal scale, I create folders per project, usually in a shared drive where the data are accessible to everyone in the project, and I diligently update my electronic lab notebooks.

Did you organize the M. truncatula mutant community screen? How many years did it go on for? How many groups participated? What were the challenges of coordinating such a large project?

One of the biggest mutagenesis screens I participated in was the annual Medicago truncatula Tnt1 transposon insertion screening that took place at Noble for about 10 years and in which I had the opportunity to interact with multiple groups within Noble external community. Initially, we screened for two symbiotic processes — nodulation and mycorrhization. Observations, nodule number, color, morphology, leaf and root phenotype were recorded as part of a database. Big screens are challenging because the number of plants screened is high, and each person has a different background. Their experience/expertise level determines how you phenotype the plants. I screened so many lines that I lost count!

What in your experience are some of the best practices for setting up a GWAS?

Last year alone, I helped conduct two Genome Wide Association Studies, which are large-scale studies and in Medicago include 226 accession lines currently. One was in a highly controlled environment, such as agar plate and the other in soil (pots) in a controlled growth room where resource availability is non-homogenous. Of course, it’s harder in soil since it takes more time, material and manpower to setup. Since the plants resource availability is not the same, even the plant position, air and light intensity play a crucial role in the experiment. To alleviate these problems, we rotated the plants within the growth chamber and used a random block design to reduce variance. To ensure its success, you need to constantly be monitoring plant health for the entire duration of the experiment.

Any advice for grad students and postdocs about to undertake such large-scale projects?

Planning is the most important requirement. Get your material ready before you start the experiment, coordinate with your team and make sure to get feedback from everybody, then take the feedback into consideration in the planning stages. Also communication is crucial.

Sonali Roy, Ph.D.
Former Postdoctoral Fellow