MECHANISMS OF SURFACE WATER SURVIVAL IN PLANT PATHOGENIC BACTERIA

Project Plan Goals:Goal 1.1: Determine the core metabolism necessary for the Ralstonia solanacearum species complex to survive in pure water to broaden our understanding of how these pathogens can transmit via contaminated irrigation water.Objective 1: Categorize all water survival factors (genes that support or hinder water survival as determined by our forward genetic screen) based on gene function using the Gene Ontology Resource.Objective 2: Determine which of these water survival factors are part of the core genome of the RSSC using OrthoMCL pangenomic analysis & BLASTP.Objective 3: Associate the water survival factors with their metabolic pathways using MetaCyc to create a core water survival metabolic network.Goal 1.2: Determine the up- and down-regulated genes controlled by core water survival transcription factors in the RSSC during survival in pure water to refine our model of these pathogens can persist in contaminated water systems.Objective 1: Create targeted knockout mutants in the Ralstonia pseudosolanacearum GMI1000 strain, targeting the genes RS RS10425 and phoU.Objective 2: Set up water microcosms with wild-type and targeted knockout strains & sample them out to 30 days for outgrowth and RNA sequencing.Objective 3: Identify differentially expressed genes within the RNA sequencing data across strains and timepoints.Goal 2.1: Determine the presence or absence of water survival factors in the Burkholderiaceae to understand how new and emerging Burkholderiaceae pathogens may survive and spread in their environment.Objective 1: Create a gene list from our genetic screen (RB-TnSeq) data that will include all genes that supported water survival in one or more of the three species evaluated.Objective 2: Use BlastP to determine the presence or absence of the genes in the gene list across the Burkholderiaceae.Goal 2.2: Infer the evolutionary history of water survival factors using synteny analysis to determine if water survival factors have been vertically inherited or have potential to be horizontally transferred within a community.Objective 1: Compile all of the GenBank files that contain the sequence and gene annotation data that will be imported into our synteny analysis tool, clinker, and filter out all genes with incomplete/broken sequences due to insufficient assemblage of the genome.Objective 2: Run the synteny analysis for all genes that passed our quality control metrics and analyze the results.Goal 2.3: Characterize the selection pressure on water survival factors in the Burkholderiaceae to determine what genes are under stabilizing selection and determine what genes would be ideal targets for the development of novel control strategies of pathogens. Objective 1: Create gene alignment files for all of the identified and conserved water survival factors.Objective 2: Run the Tajima's D test in the R statistical computing software and determine the synonymous & non-synonymous mutation ratios for each gene.Career/professional development goals:Goal 1: Develop an inclusive pedagogy and teaching philosophy to help me serve a diverse community of students.Objective 1: Complete the Future Undergraduate Science Educators program at UC Davis.Objective 2: Continually participate in workshops provided by the Center for Educational Effectiveness at UC Davis.Goal 2: Broaden my mentorship toolset to train future scientists.Objective 1: Continue to mentor students through institutions such as the Society for the Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS).Objective 2: Co-mentor students in collaboration with Professor Lowe-Power and train them to be independent scientists in our lab.Goal 3: Refine my technical and scientific skillset to ensure my trainees will provided with knowledge on cutting-edge techniques, as well as ensure they are using the best-practices with already established techniques.Objective 1: Attend the Joint Genome Institute Microbial Genomics & Metagenomics workshop to develop my computational skills.Objective 2: Present my work at least annually to my department and at least annually at research conferences to seek feedback on how I can improve my methods and techniques.Objective 3: Meet regularly with my mentors and discuss any technical problems I have been having in my research.Goal 4: Establish a network that consists of professors from Primarily Undergraduate Institutions (PUIs)to ensure that I can maximize my preparation for a professorship at a PUI.Objective 1: Meet regularly with my undergraduate research advisor, Professor Elinne Becket, and seek her advice on how to plan my professional development as a graduate student and post-doctoral scholar to ensure I am preparing for a professorship at a PUI.Objective 2: Obtain institutional support from the California State University (CSU) system (ideally in the form of becoming a CSU Chancellor's Doctoral Incentive Program Fellow) to further prepare myself for a professorship at a PUI.