REU: Systems Biology of Plant and Microbiome

Center for Root and Rhizobiome Innovation  –

For information contact

Nicole Busboom

Outreach Coordinator, Nebraska EPSCoR

2019 Plant & Microbiome Students at REU picnic
2019 Plant & Microbiome Students at REU picnic

Who should apply

Related fields

  • Plant Pathology
  • Biochemistry
  • Biology
  • Agronomy and Horticulture
  • Biology Systems Engineering
  • Chemistry
  • Genetics


Participation in the Nebraska Summer Research Program is limited to students who meet the following criteria:
  • U.S. Citizen or Permanent Resident
  • Current undergraduate with at least one semester of coursework remaining before obtaining a bachelor's degree

See Eligibility for more information.

How to apply

Follow the application steps to submit the following materials.

About the Program

The Center for Root and Rhizobiome Innovation (CRRI) will establish and develop tools and technologies for more rapid, precise, and predictable crop genetic improvement that complement methods currently used by biotechnologists and plant breeders.  These innovations are needed because of the urgency and enormity of challenges facing global agriculture, including the need to feed a rapidly growing population in the face of extreme climate variations and limitations in water and soil vitality.  

CRRI research will be structured around a systems and synthetic biology core to generate and iteratively improve network models of plant metabolism for predictable outcomes from genetic modifications.  CRRI’s systems and synthetic biology research will be applied to the study of root metabolism and its influence on root-interactions with soil microbes for improved plant health.    

Research will focus on root metabolism in maize, a plant genetic model and important crop species, but findings will be broadly applicable to other plants and crop species.  CRRI will develop and use fundamental knowledge to create translational products with far-reaching impact on plant and microbial biology and global agriculture.


  • Competitive stipend: $5,000
  • Suite-style room and meal plan
  • Travel expenses to and from Lincoln
  • Campus parking and/or bus pass
  • Full access to the Campus Recreation Center and campus library system
  • Wireless internet access

Learn more about academic and financial benefits.


  • Department seminars and presentations
  • Professional development workshops (e.g., applying to graduate school, taking the GRE)
  • Welcome picnic
  • Day trip to Omaha's Henry Doorly Zoo
  • Outdoor adventures
  • Research symposium

Mentors and Projects

Investigating Plants Photoprotection Characteristics

The Glowacka Lab ( investigates the most fundamental process for life on earth, photosynthesis. We seek to understand how we can modify photosynthesis by genome alteration or/and breeding for improving plant growth under abiotic stresses to secure food and bioenergy production in the future. Particularly, we focus on the mechanism of photoprotection.  However, photoprotection protects plants from excessive light energy by its harmless dissipation as heat, it can also compete for energy with photosynthesis when the light is limited (e.g. overcast day). Since the speed of induction and relaxation of photoprotection can have a significant effect on plant growth, we are interested in defining desired characteristics of photoprotection under varied growth conditions.

Dr. Tomas Helikar Biochemistry

Utilizing Computational Modeling to Understand Plant Systems

Students would work with multiscale computational models of plant systems can enable better understanding of metabolic processes, relationships between genotype and phenotype, and impact of cellular and environmental factors. We have developed a comprehensive multi-scale metabolic model of maize root and its mutualistic soil microbe community. Simulation results predict the uptake of maize root secretions by soil microbes and vice versa. Transcriptomic analyses of maize root under varying nutrient conditions and root regions with highly expressed genes unveil more flux carrying reactions than lowly expressed genes. The REU student(s) will work with our team to 1) use the model to design novel hypotheses about manipulating microbial metabolism to improve the maize growth, and 2) develop computational models of additional soil microbes.

Dr. Rajib Saha Chemical and Biomolecular Engineering

Using Mathematics to Design Genetic Circuits to Modify Root-Microbe Interactions for Increased Yield

The interactions which occur between the root of a plant and the microbes which inhabit the root and the surrounding soil are critical to the well-being of a plant as these microbes (collectively called the rhizobiome) perform a wide range of beneficial functions for their associated plant, such as the provision of nutrients, the retention of water, pathogen resistance, and generally increased plant health and growth. More recently, it has been discovered that this interaction proceeds in both directions, and that the plant provides nutrients, called exudates, to support its microbial community. These interactions are, yet, an untapped method of improving crop yield, and can be described mathematically. The goal of this project is that by using mathematical descriptions of these interactions which occur in maize (corn) and a tool for the design of genetic circuits, multiple plasmids might be designed through experiments performed in computers (in silico) which show in silico potential to increase plant growth by the manipulation of root-rhizobiome interactions. Candidate plasmids will be designed using bioparts (promotors, transcripts, terminators, etc.) identified during the course of the REU, with the design being performed using an in silico tool for genetic circuit design. These designed plasmids will be evaluated using a Genome Scale Model (GSM) of model of metabolism. Plasmids showing in silico at the end of the REU will then be presented to collaborating researchers for potential incorporation into in-organism maize root experiments.

Dr. James Schnable Agronomy and Horticulture

Optimizing in silico Plasmid Design and Evaluation

While individuals specialize, each member of the Schnable lab gets at least some experience writing computer code, employing molecular biology techniques, working with living plants in the greenhouse, and conducting fieldwork. As a result of the diverse set of collaborators we work with – applied plant breeders, biochemists, engineers, computer scientists, food scientists, and statisticians – each member of the lab also gains experience communicating both within and across scientific disciplines, as well as to diverse non-scientific audiences. This cross training produces scientists who are equipped to both understand and address the complex and far-reaching problems our world will face in coming decades. 

Dr. Bin Yu Biological Sciences

The Molecular Mechanisms of RNA Metabolism and Functions

Student would work to understand the molecular mechanisms underlying small RNA metabolism and function. RNA silencing is a process triggered by ~21-24 nucleotide RNAs to repress gene expression. The Yu lab is interested in understanding of the mechanisms governing RNA silencing and development of RNA silencing based-technologies that can be used to improve crop traits.