This pilot program is aimed at building stronger reciprocal ties between agricultural research at 1862 and 1890 Land Grant Universities (LGUs) by expanding access to research and educational resources, providing greater opportunities for student career development, and promoting diversity in US agricultural sciences, industries, and production. Student participants will conduct research projects in fundamental and/or applied aspects of plant sciences. We envision research projects may span lab-based research, computational biology, and field-based production research with training in areas including molecular biology, biochemistry, genetics/genomics, and physiology.
Participants will develop and implement a summer research project under the guidance of the faculty mentor and his/her research team. Students will also participate in weekly interactive meetings with UNL faculty members on development of scientific research and communication skills and with experts in academic and industrial agricultural research, extension, and crop and livestock production.
To meet the needs of non-traditional students who are unable to dedicate a summer in Nebraska, we will also implement a hybrid model where the student conducts research at their home institution in a collaborative arrangement between faculty at UNL and their home university.
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
The student will have the opportunity to work in an applied plant breeding program focusing on improving winter wheat, barley, and triticale. Using wheat as an example 20% of the calories and 20% of the protein consumed by humans is from wheat. Depending upon the student’s background and interest, he or she can study the genetics of winter survival, disease, insect, or herbicide tolerance, the floral biology needed for hybrid wheat (will depend on the student’s arrival date as flowering occurs in mid to late May), or end-use quality (primarily does an experimental line make a good loaf of bread).
High throughput genotyping and phenotyping are becoming key aspects of experimental line selection and advancement, so the student can also work with experts in these fields. The student will work with a range of scientists and students from different backgrounds. No prior experience with any of these tools is expected or required. They will be learned onsite or remotely.
The student participant will conduct lab- and field-based research aimed at transferring metabolic pathways for high-value traits for food, feed, industrial, or bioenergy uses in crops such as soybean and sorghum. The student will participate in metabolic engineering experiments using synthetic biology tools and gain exposure to biochemistry, molecular biology, and analytical chemistry for biotechnological development of crops with enhanced value. The student will also have the opportunity to monitor the agronomic properties of engineered crops in field test plots.
Understanding the protection of photosynthesis apparatus from abiotic stresses
Photosynthesis, one of the most important biological processes, feeds directly or indirectly almost all life on Earth. Therefore, it is urgent to gain the understanding 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. The student will investigate the plant physiological characteristics under control and stress conditions. The project will include measuring plants photosynthesis based on chlorophyll fluorescence, analyzing images and investigating the biochemical changes in the leaves.
The student will assist with collecting the samples from the field, taking the fluorescence images of leaf fragments or whole plants. The student will analyze the data using dedicated software and preparing the graphical representation of collected data. The student will have the opportunity to work with image analyzing software such as MATLAB and ImageJ (no prior experience with these tools is required).
Dr. Joshua Herr
Department of Plant Pathology; Center for Plant Science Innovation; School of Biological Sciences - Genetics, Cell, and Molecular Biology; and Quantitative Life Sciences Initiative
Increasing crop yields through the application of host-specific arbuscular mycorrhizal fungi
The student involved with this project will facilitate a greenhouse experiment when they will grow different varieties of dry beans and will apply a suite of arbuscular mycorrhizal and endospore-forming fungi known to promote plant growth and increase yields. The student will measure plant biomass growth and seed weight and quality. The project will then consist of the extraction of DNA and RNA in the laboratory. After sequencing of the nucleotides, the student will quantify plant and fungal gene transcription with host-symbiont pairings that correspond to increased growth and yields.
The student involved with this project should have a desire to partake in greenhouse, laboratory, and bioinformatic aspects of the study. A proficiency in the bash shell and R is highly recommended, but not required. What is required is a desire to learn and a passion for scientific discovery.
Breeding experience for undergraduates in generation of novel varieties of popcorn and sweetcorn
The project is a continuation of a multi-pronged approach to breed several new varieties of popcorn and sweetcorn using public germplasm. The overarching goal is to provide undergraduates with hands-on experience in basic field techniques in maize breeding while also exposing them to hands on lab screening techniques using primer design, DNA extraction, PCR and protein analysis.
There are three applied aims including breeding of a variety of novel colored, sugary1 and shrunken 2 sweetcorns, breeding of quality protein sweetcorns and breeding a variety of colored, quality protein popcorn lines. Many and varied F1s have already been made and F2s are being generated in the greenhouse. The project will capitalize on these with the visual and molecular screening of F2 ears and propagation of the next generation in the field. The ultimate goal will be hybrid production in each of the above categories.
Understand the regulation of plant gene expression at the single-cell level
The student participant will study the regulatory mechanisms controlling the expression of each plant gene in each cell composing the root. This project will contribute to our understanding of the role and regulation of plant genes in controlling 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 molecular technologies) and in bioinformatics.
The students will assist in the use of single-cell biotechnologies on plant roots, and he/she will analyze his/her results to create a unique understanding of the role of plant genes during root development. His/her dataset will be integrated with other existing plant root transcriptomes to provide a deeper understanding of the evolution of plant gene expression. As part of this internship, the student will develop skills in cell biology, molecular biology, and bioinformatics.
Understanding plant defense mechanisms to insect pests
This project will focus on understanding endogenous plant defense mechanisms and to better understand the behavior and chemical ecology of multi-trophic interactions between plants, pests, or beneficial species. Undergraduate students will be given a specific project to complete that will require them to become familiar with insect bioassays, feeding behavior analysis, RNA techniques, and to identify and quantify the different defense-related phytohormones or blends of volatile organic compounds (VOC) that can attract natural enemies of the attacking herbivores.
Effects of mycorrhizal composition on drought tolerance of Nebraska sand hill prairie grass species
Biomes worldwide are experiencing dramatic shifts in rainfall regimes and the frequency and severity of drought, which has consequences for plant productivity in natural and agricultural systems. Arbuscular mycorrhizal fungi colonizing grass roots play important roles in enhancing nutrient uptake, but less is known about their effects on drought tolerance of grasses. This REU project will involve conducting greenhouse experiments using prairie grass species occurring on a natural water availability gradient in the Nebraska sandhills. We will manipulate mycorrhizal colonization and water stress to test the hypothesis that mycorrhiza enhance drought tolerance of grasses, and explore the underlying physiological mechanisms.
If only remote research is possible, the REU student will observe remotely the data collection in the greenhouse and contribute to collection and analysis of phenotypic data on the harvested experimental plants. This project will advance our understanding of how plant-fungal interactions may improve resistance of grasses and cereal crops to water limitation.
Plant and soil microbiology - studies on the mysteries of the underground microbiome
The student participant will work as a team member with others on lab- and field-based research aimed at determining the role that key soil bacteria and fungi play in enhancing yields and stress tolerance. The microbes will either come directly from field experiments or from our extensive culture collection.
The student will participate in microbe isolation, measurement of plant physiological and morphological characeristics, DNA sequencing, PCR and other lab methods. They will learn the basic techniques in microbiology, plant biology, field measurements and image analysis. The work will involve working outside in agricultural fields and inside in the laboratory.
Mapping genes controlling trait variation in corn and sorghum
The student will be engaged in phenotyping efforts to measure traits in diverse panels of corn or sorghum and then use the data they generate to map the genes that control these traits in one or both of these crop species. Depending on the student’s background, interests, and whether the project is conducted remotely or on-site, measuring traits may include physical measurements of plants in the field or seedlings grown in the greenhouse, manual measurements from photos collected in the field or greenhouse or using computer vision and artificial intelligence software tools to have computers measure traits directly from images and other sensor data. The measurements the student generates will then allow them to conduct a genome wide association study and identify potential candidate genes controlling their trait of interest.
The student will have the opportunity to work with and collaborate researchers from a range of academic backgrounds (biology, statistics, engineering, and computer science) and develop familiarity with Python, R and the Unix command line (no prior experience with these tools expected or required).
Dr. Mark Wilkins
Department of Biological Systems Engineering, Department of Food Science and Technology
Bioplastics production from novel lignins
The student participant will look at conversion of lignins from plant cell walls that have modified structures compared to wild-type. These lignins would include those from natural mutations, particularly brown midrib corn and sorghum varieties, and those achieved through genetic manipulation. In particular, the student would look at how utilizing lignins that are constructed from aromatic aldehydes (as opposed to aromatic alcohols) and/or have increased cinnamic acid content affect yields of PHAs from microbial cell culture. Preliminary work indicates that these lignins results in higher PhB yields as opposed to wild-type, but only a few cell cultures have been done.
Connecting fungal growth in living plant cells with host innate immunity suppression
Fungal phytopathogens cause devastating plant diseases and a handful threaten global food security. One of the most notorious of these is the blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae), which destroys 10-30 % of rice harvests each year and is an emerging problem on wheat. M. oryzae is a class of phytopathogen called a hemibiotroph. Hemibiotrophs grow for several days in intimate contact with living host plant cells before the onset of disease symptoms. In M. oryzae, this early biotrophic growth stage is characterized by the elaboration of intracellular invasive hyphae that are wrapped in host-derived membranes, forming a biotrophic interface for deploying plant-immune suppressing protein effectors and for exchanging nutrients. An open question in plant pathology lies in not understanding the molecular decision-making processes balancing invasive hyphal growth, biotrophic interfacial integrity and host innate immunity suppression during the fungal colonization of living host plant cells. Disrupting this balance might reveal novel mitigation strategies or sources of host resistance.
The student involved with this project will generate mutant strains of M. oryzae, lacking genes required for balancing fungal growth with plant defense suppression, and characterize them by 1) live-cell imaging using state-of-the-art scanning laser confocal microscopy; 2) scanning electron- and transmission electron microscopy; and 3) genome-wide transcriptomic, proteomic and metabolomic approaches. The goal of the project will be to provide a deeper understanding, at the molecular level, of how the cells of one organism thrive in the cells of another, thus potentially identifying pathogen weak points that can be exploited. No prior experience is required.
Understand the regulatory regions in controlling gene expression and agronomical traits of interest
Agronomically important traits were under complex genetic control.
Depending on the student’s background and interests, she/he will be working on generating or analyzing multi-Omics data to untangle the intricate patterns in controlling phenotypic variation. For the Omics data, the student will be focusing on studying active chromatin regions, especially the enhancers or promoters that are actively involved in gene regulations. The student will have the opportunity to work with researchers from a range of academic backgrounds. They will also learn how to use computational tools to establish the connections between the multi-Omics data and traits of interest.
Dr. Bin Yu
School of Biological Sciences, Center for Plant Science Innovation
Non-coding RNAs are regulatory RNAs that play critical roles in regulating gene expression and chromatin stability. They play critical roles in various biological processes such as development and responses to various environmental signals However, related regulatory processes and mechanisms are still less understood. In this project, the student will work with other fellow researchers to combine gene co-expression network and protein interaction data to identify candidate genes involved in regulating the levels of miRNA and/or other non-coding RNAs. Moreover, the student will also work on the functional analyses of the candidate genes. The student will have opportunities to learn molecular biology, bioinformatics, RNA biology, biochemistry and cell biology
Bioinformatics study in mRNA splicing to improve gene function annotation in crops
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 exons 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 characterizing 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 RNA-seq datasets of crops. This project will provide fundamental knowledge to gene annotations products with far-reaching impact on plant biology and molecular biology.