ITR: Understanding Stress Resistance Mechanisms in Plants: Multimodal Models Integrating Experimental Data, Databases, and the Literature

Virginia Polytechnic Institute And State University, Blacksburg VA

Investigators

Abstract

Plants have evolved to cope with a variety of environmental stresses, including drought, heat, cold, salt, pathogens, and insects. The imposition of stress on a plant results in the marshaling of genomic defense mechanisms. Some defense mechanisms are common to the response to multiple stresses (e.g., drought and salt), while others are more specific. Defense mechanisms may interact collaboratively to combat a stress or may work independently to repair multiple kinds of damage inflicted by stress. This research proceeds on the premise that functional genomic and bioinformatics approaches together with data from drought stress experiments and information from multiple biological information sources can elucidate relationships among and within stress mechanisms. This project will capture these relationships in representations or models called multimodal models. Sources of biological information that will be utilized include (1) data from drought-stress experiments, especially gene expression data from microarray hybridizations; (2) sequence, protein, and other databases; and (3) the biological literature. Multimodal models will represent these multiple aspects of biological knowledge and of biological systems themselves: responses over time; response variation by subcellular compartments; uncertainty (our lack of complete knowledge of cell state); and the dynamic changes in biological information due to the boom in biological data and knowledge. These models are readily visualized, explored, analyzed, and extended via computational means. Current models for drought stress response will be available via the project web site. The microarray experiments for studying drought stress in loblolly pine and Arabidopsis thaliana (a model plant for biological research) will be designed, managed, and analyzed by the Expresso system, a microarray experiment management system for experimental design, data capture, and data analysis. The experimental and computational methods used in this research will have an impact on the ability of biologists to address additional complex, interrelated hypotheses using microarray technology and other tools of modern genomics. The multimodal networks will have predictive power that will enable biologists to explore hypotheses computationally in advance of experiments, to obtain estimates of probabilities associated with various drought response mechanisms given hypothesized drought stress conditions, to decide on future experiments based on the estimated likelihood of a large yield of information from the experiments, and to serve as the basis for mathematical models that have more quantitative predictive power. Enhanced understanding of responses to drought and other stresses in plants will ultimately benefit agriculture and forestry in the form of hardier crops and trees.