In eukaryotes, small RNAs (20–30 nt) derived from double stranded RNA precursors direct proteins to regulate chromatin function, transcription, RNA stability, and translation through sequence-targeted mechanisms termed RNA silencing. Two main categories of plant small RNAs, microRNAs (miRNAs) and short interfering RNAs (siRNAs), guide cleavage of mRNA and posttranscritionally silence expression of genes critical to growth and responses to environmental cues. Plant innate immune receptors, encoded by large families of plant resistance genes (R-genes) recognize pathogen effectors and induce the cell-death hypersensitive response. While these receptors protect plants from diverse pathogens, their large numbers and inherent cell death activity require strict regulation; high levels can induce autoimmune responses and severely reduced growth, and low levels produce ineffective resistance. We recently identified several miRNA families that silence R-gene expression. We hypothesize that these miRNAs balance plant growth and fine-tune R-gene expression following pathogen infection. The project uses molecular-genetic, genomic and CRISPR/Cas9 gene editing approaches to determine mechanisms of RNA silencing for plant growth and defense. The results of these studies have broader implications for regulation of resistance genes for optimized crop protection against pathogens. A better understanding of the role of silencing in fine tuning disease resistance would allow targeted activation or repression of innate immune responses and more effective deployment of resistance genes for crop protection.
This is an excellent opportunity for a student interested in becoming proficient with a variety of techniques fundamental to genomic, genetic and molecular biological research. The student will work with other scientists studying silencing regulation of gene expression in response to pathogens. The student will interact with the lab’s principal investigator, Barbara Baker and will work with a postdoctoral researcher, staff research associate and graduate and undergraduate students. The undergraduate researcher will be involved in validation of transgenic lines mutated in different RNA silencing pathways to test the role of silencing in pathogen defense. The student will learn analysis of CRISPR/Cas9 gene edited lines, recombinant DNA techniques: PCR, E. coli transformation, plasmid purification, plant genetics, and plant DNA/RNA extraction and apply their knowledge of computational approaches for sequence analysis. In addition, the student will have the opportunity to attend and participate in lab meetings and seminars.
The student should have a desire to learn and conduct basic research and a solid understanding of molecular biology concepts. Some prior experience with molecular biology techniques is desirable and theoretical familiarity with such techniques is expected. We are seeking interested students with a background in computer science or bioinformatics for genome and transcriptome analyses. The student must be responsible, conscientious, attentive to detail and able to relate the details of her/his work to the larger objectives of the project. Candidates who have completed core classes for biological or computer science majors are preferred.