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
Investigating the photoprotection characteristics under control and stress conditions
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.
The project will include measuring plants photoprotection based on chlorophyll fluorescence, analyzing images and investigating the biochemical changes in the leaves. It is expected that, over time, the student will master basic skills and be able to take on more responsibility and independence.
Potential student tasks and responsibilities: The student will assist with collecting the samples from field, taking the fluorescence images of leaf fragments or whole plants using the fluorescence imager, analyzing the data using dedicated softwares and preparing the graphical representation of collected data.
Student qualifications and characteristics: Interest in plant biology; reliability; ability to communicate clearly and follow instructions; attention to detail, particularly for keeping lab notes; engaged and excited to learn; comfortable asking questions; good team player.
Developing and analyzing the transcriptome of each cell composing the maize root biology
This project is important to access because it will help to understand the role of each maize gene in regulating root development and root cell differentiation.
To reach his/her objective, the student will benefit from the expertise of lab members in plant single-cell –omics (one of the most innovative technologies currently existing in molecular analyses) and in bioinformatics. The students will not only perform experiments in the laboratory, but he/she will analyze his/her results to create a unique understanding of the role of maize genes during root development. His/her dataset will be integrated with other plant root transcriptomes to provide a deeper understanding of the evolution of plant genes. This project is relevant to on-going CRRI efforts because it will complement the transcriptomic analyses currently conducted as part of the CRRI project.
As part of this summer experience, the student will develop skills in cell biology, molecular biology, and bioinformatics. The student will learn how to isolate plant nuclei before committing them to single nuclei RNA-seq technology. The student will learn about the various quality checks needed when performing these experiments. Upon successful isolation of the maize root nuclei, the student will use droplet systems to create independent cDNA libraries for each cell composing the maize root. Finally, upon the sequencing of these DNA libraries, the student will be introduced to the analysis of the single nuclei RNA-seq datasets.
Creating Genetic Circuit Designs Using Systems and Synthetic Biology Tools
The student will work to improve and apply a quantitative tool for the design of genetic circuits for Zea mays (known as corn or maize) plants the long-term goal of improvement of the root-rhizobiome system for improved plant health, yield, decreased fertilizer requirements, and the testing of other hypotheses which may arise. Over the REU term, the student will be familiarized with a wide variety of topics in systems and synthetic biology fields including optimization, set theory, genetic regulation, binary logic, genetic circuits, and metabolic modeling. Students will create genetic circuit designs using systems and synthetic biology tools and will be informed by models of root-rhizobiome metabolism. Their designs will be used to create a library of genetic circuit designs, including their components, associated logic flow diagrams, response patterns, and recommendations for their use.
These designs may be implemented in synthetic biology experiments which will aid in the iterative improvement of models of root-rhizobiome metabolism and the improvement of plant performance. Our laboratory contains both systems and synthetic biologists who will guide the REU student in the understanding of their work and the execution of their duties.
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.
Developing bioinformatics pipelines to the analysis of RNA-seq datasets to improve gene structure annotation in plants
Precursor messenger RNA (pre-mRNA) splicing is the process by which intron sequences are identified and excised from pre-mRNA transcripts with concurrent ligation of the flanking exons. Pre-mRNA is an important step for gene expression regulation, and gene structure information, such as exon sequences and locations, is critical in pre-mRNA splicing studies. Next-generation sequencing technology has been used in biological studies widely, including obtaining gene structure information. However, many exons, such as exon with structure variations, are challenging to be detected with current methods. Bioinformatics tools are employed to characterize gene structure information in a high-throughput fashion. It is urgent to get better bioinformatics tools to analyze next generation sequencing data to get better characterize gene structures.
The research will focus on the analysis of many RNA-seq data sets in plants using our developed pipeline and retrieve the gene structure information for plant gene annotation and evolution. Students will be introduced to several bioinformatics tools essential for data analyses. After the training, they will be able to independently utilize these resources to characterize biological variables of interest from plant RNA-seq datasets. This project will provide fundamental knowledge to gene annotations products with far-reaching impact on plant and molecular biology.