REU - Field of Phenomes

1. Plant microbiome and crop productivity (Heike Bücking – Biology and Microbiology). Increasing the efficiency with which crops absorb or utilize nutrients represents an urgent priority to ensure cost-effective and sustainable agriculture in the future. Plants are metaorganisms, and their phenotype is greatly influenced by beneficial (e.g. arbuscular mycorrhizal fungi or other endophytes) or pathogenic microbes. The students will design experiments to study the responsiveness of plants to the inoculation with beneficial microorganisms in laboratory and in field experiments, will be integrated into a collaborative research project with an industrial partner with the goal to identify potential candidates for commercialization as microbial fertilizers or pesticides, and will get hands-on-experience in labeling experiments, RNA and DNA extraction, metagenome, transcriptome analysis, qPCR and bioinformatics.
    
2. Grapevine phenotype and genotype (Anne Fennell, Plant genomics: Genome and Phenome). Image acquisition, quantitation, and trait analyses are critical to gain an understanding of the genetics underlying phenotypic variations. Students will use a replicated F2 grapevine population, located in Brookings, SD and Greenfield, CA.  This population segregates for many morphological, physiological, metabolic and fruit quality traits; providing the opportunity for genetic trait architecture and genotype by environment analyses. This population has been genotyped and an integrated dense rhAmpSeq and SNP map exists allowing the students to acquire images or physiological data, process the data and conduct quantitative trait loci analysis to begin dissecting the regions of the genome and candidate genes that are involved in the expression of the phenotype. This will help the students to develop an understanding of the genomic basis of phenotype variation in a well characterized perennial plant system.
    
3. Molecular characterization of mycoviruses (Shin-Yi Marzano – Biology and Microbiology). The students will work on the identification and characterization of mycoviruses in different fungi. Mycoviruses are widely spread, and can have a significant impact on fungal phenotype, and for example affect the pathogenicity of crop pathogens. However, mycoviruses are not well studied. The students will be trained in techniques such as RNA extraction, sequencing analyses and bioinformatics.
    
4. Hormone signaling in root nodules (Senthil Subramanian – Agronomy, Horticulture, and Plant Science Department).Spatiotemporal transcriptome and hormone output imaging datasets have uncovered key mechanisms that regulate hormone balance during soybean nodule development. For example, microRNA160, a small regulatory RNA, dictates developmental stage-specific sensitivities to the plant hormones auxin and cytokinin, and directs nodule development. We have adapted two photon induced fluorescence-based concurrent imaging methods to simultaneously detect auxin, cytokinin and miR160 activities in living nodules at different stages of development. The REU trainees will conduct experiments using hormone and miRNA output imaging, analysis of high throughput sequencing datasets and computational analysis to integrate transcriptome and silenceome datasets to discover the roles of miRNAs in nodule development.
    
5. Water stress in alfalfa (Yajun Wu – Biology and Microbiology Department). The students will work on a project to characterize a novel alfalfa germplasm with high water use efficiency under drought stress. The student will be trained in techniques such as plant culture, implementing water stress treatments, quantitative measurement of water content and transpiration rate, examination of leaf morphology by microscopy, plant hormone and activity measurements and final data analysis. The students will learn how phenotypic variations can reveal potential regulatory mechanism in the water use efficiency of plants.
    
6. Engineering of photosynthetic cyanobacteria (Ruanbao Zhou – Biology and Microbiology). Cyanobacteria have great potential as cellular factories, due to their ability to fix CO₂ and photo-oxidize water, their nutritional simplicity, and their amenability for genetic manipulation. We use a synthetic biology approach to develop a suite of engineered Anabaena strains that are separately capable of directly converting CO₂ and H₂O into various hydrocarbons or other commodity chemicals, such as limonene. Through genetic alteration of target metabolic pathways, the students will redirect Anabaena’s carbon flow from producing stored precursors (i.e. lipids and polysaccharides) to the direct production of excreted end products. The students with get hands-on training in genetics and molecular biological techniques, such as PCR/RT-qPCR, gene cloning, gene inactivation and transfer, plasmid construction, genetic transformation, recombinant protein expression, Western blots and other molecular techniques

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