SPLS Tuesday Seminar - Raising the BAR for Hypothesis Generation in Plant Biology: Guard Cell Drought Transcriptomes Use Case

Dr. Nicholas Provart
University of Toronto
Tuesday, March 14, 2023 - 4:00pm
Marley 230 & Live on Zoom https://arizona.zoom.us/j/88614287572 Password: spls2023

Join us at 3:30 p.m. in the Marley lobby for refreshments
The presentation will begin at 4:00 p.m. in Marley 230
A live broadcast is available via zoom: https://arizona.zoom.us/j/88614287572  Password: spls2023

We have developed tools, available as part of the Bio-Analytic Resource (BAR) at http://bar.utoronto.ca, for exploring large data sets from plants, to allow deeper insights into biological questions. My lab’s three visual analytic tools for transcriptomic data (eFP Browser, ePlant, and eFP-Seq Browser) allow for rapid access to comprehensive gene expression compendia we have curated for identifying tissues, cell-types, or perturbations in which a gene is active or alternatively spliced. Interactions, be they protein-protein or regulatory, create networks. We have developed new tools for exploring such data, either from large collections of experimentally-supported protein-protein or protein-DNA interactions or from predicted interactions, including protein-protein interactions inferred from molecular docking studies. Our lab is also interested in generating data to help understand drought responses and we have modified the INTACT system to isolate transcriptomes from guard cells and whole leaves of plants subject to slowly developing drought. Using some of the above-mentioned tools and other bioinformatic analyses, we have been able to show that guard cells exhibit unique patterns of response both at early and later stages of drought. Thermal imaging of reverse genetic lines, prioritized in part using BAR tools, suggests the physiological importance several differentially expressed genes in guard cells from droughted plants. 

Nicholas Provart is a full professor of Plant Cyberinfrastructure and Systems Biology and is chair of the Department of Cell & Systems Biology at the University of Toronto. Currently his Bio-Analytic Resource (BAR) at bar.utoronto.ca, comprising tools for coexpression analysis of publicly-available gene expression data, cis-element prediction, identifying molecular markers, generating “electronic fluorescent pictographic” (eFP) representations of gene expression patterns, and exploring protein-protein interactions in Arabidopsis and other plants, receives 4M page views a month by researchers worldwide. He is one of the founding members of the International Arabidopsis Informatics Consortium, is president of the Multinational Arabidopsis Steering Committee, and is teaching two MOOCs on Bioinformatic Methods on Coursera.org, with a 3rd released in December 2018 and a capstone rounding out a Plant Bioinformatics specialization in 2019. He was a Clarivate Highly Cited Researcher for three years.