Research Associate

This individual will conduct laboratory-based basic and applied research on fire blight bacterium Erwinia amylovora. The candidate will work on the following basic research aspects of this pathogen — particularly focused on: (I) Determining microbiome composition in fire blight cankers and shoots (both in silico by sequencing and in vitro by microorganism isolation), including sequencing to identify fungi, bacteria, and viruses; and (II) Characterization of plant-pathogen interaction in fire blight cankers and apple/pear shoots using omics and analytical chemistry tools such as but not limited to: dual RNA sequencing, gene expression, metabolomics, proteomics, genome/gene sequencing, E. amylovora functional genetics and utilization of droplet digital PCR, qRT-PCR, and HPLC-MS or GC/MS assays (from sequence generation or molecule extraction to data analysis and presentation and publishing). The work also includes optimizing and conducting other plant and pathogen assays that reveal the physiological status of both plant and pathogen during interaction in bark, shoots, and other tissues on apple and pear. It includes gene annotation and analysis of genome/gene sequences for gene(s) of interest, characterization or bactericide resistance mutations, detection of compounds with analytical chemistry tools, and elucidation of fire blight survival and infection sources. The aim is to conduct research on the ability of E. amylovora to navigate different host tissues and elucidate plant-microbe interactions during tissue invasion shifts with focus on virulence factors, stress-related genes, and apple/pear cultivar responses (including E. amylovora gene deletion mutants). The candidate is expected to learn and use modern available DNA, RNA, transcriptome, and/or metabolome analysis software platforms and pipelines, conduct data analyses, and perform tasks independently. The successful candidate is expected to independently process samples and collect and analyze data; maintain and store pathogen cultures; design, organize, and manage lab experiments; budget and order laboratory supplies; optimize and implement DNA, RNA, and metabolomics protocols, gene expression assays, conduct DNA/RNA extractions and experimental trials including any other closely associated tasks related to this research. Required Qualifications

Master’s degree in Plant Pathology or related field. (An exception may be granted for individuals with a bachelor’s degree and significant relevant experience.) Skills in basic microbiology, bacteriology, plant pathology, molecular biology, bioinformatics, plant disease diagnostics, and plant-pathogen interactions; quantitative PCR platforms for pathogen detection and quantification, gene sequencing, and expression, gene-editing, and optimization of these assays. Skills in microbiome and genome sequence mining and analyses, antiSMASH analysis, CASymes analysis, effector analysis, BUSCO phylogeny, fastANI analysis, primer design, pathogen characterization, plant inoculation methods, pathogen sensitivity assays. Strong scientific writing and data analytical skills with a good track record of project data collection in notebooks, data storage, and sharing. Skills in conducting statistical analyses with various software independently. Skills with microorganism manipulation in vitro and in vivo. Valid driver’s license. Preferred Qualifications

Ph.D. in Plant Pathology with research experience focused on bacterial and/or fungal pathogens of plants with a focus on transcriptome analyses and omics. Demonstrated research experience on bacterial and/or fungal pathogens of plants with a focus on identification and characterization of pathogens of plants, and on development and use of diagnostic and quantification assays for bacterial and/or fungal plant pathogens focused on pathogen biology, ecology, management, and epidemiology. Advanced use of basic cell and molecular biology techniques and analyses software including DNA/RNA manipulation (extraction from difficult samples), cDNA synthesis, gene expression analysis, gene and genome sequencing, gene and genome phylogeny, nucleic acid extraction, cloning, gene mutations, yeast two-hybrid screening, gene knockouts, and scanning electron microscopy. Research experience in plant-microbe interactions, plant immunity responses to pathogens, plant pathogen gene expression, gene sequence analysis, and functional genetics assays, Erwinia amylovora mutant characterization. Experience and willingness to write grant proposals and a good record of refereed research publications on plant pathogens. Virginia Tech is an equal opportunity employer and does not discriminate against employees, students, or applicants on the basis of age, color, disability, sex (including pregnancy), gender, gender identity, gender expression, genetic information, ethnicity or national origin, political affiliation, race, religion, sexual orientation, or military status, or otherwise discriminate against employees or applicants who inquire about, discuss, or disclose their compensation or the compensation of other employees or applicants, or on any other basis protected by law.

#J-18808-Ljbffr