Biologically active chemicals are the basis of most known therapeutics and are powerful tools to study cell biological processes. However the discovery of new bioactive compounds and characterization of their molecular targets remain a challenge. We are using small molecule and natural products libraries to identify novel compounds that affect animal development and study their modes of action. We have established a high-throughput automated platform for chemical and functional genomic screening that accommodates both cell-based and whole-organism (e.g. microbial, worm and zebrafish) assays. We are focusing on potential disease therapeutics (e.g. cancer, diabetes) and broad-spectrum anthelmintics (to target parasitic nematodes that affect human, crops, and livestock) using the free-living nematodes C. elegans and the distantly related P. pacificus as model animals, since they offer a rapid and powerful platform for lead compound discovery and mode of action studies. Given the short life cycle of the worm, our high-throughput screening (HTS) platform enables one person to screen 20,000 chemicals per week and perform one genome-wide RNAi screen every 2 weeks. Results are scored using automated image analysis with DevStaR, a software package we developed that employs computer vision and machine learning to quantify embryonic lethality in mixed-stage worm populations (White et al., 2013). We validated our screening approach in a pilot screen of an FDA-approved drug library, which confirmed the effects of known anthelmintics on C. elegans and P. pacificus. We then screened a library of ~32,000 small molecules that were selected using a computational approach to predict bioavailability in nematodes (Burns et al. 2010). Preliminary analysis based on worm survival and developmental phenotypes suggests a 4% hit rate. Positive hits will be assayed for toxicity in zebrafish and mammalian cells. To uncover molecular targets of bioactives and mechanisms of resistance, we will use forward and reverse genetic screens to identify suppressors (or enhancers) of chemical sensitivity. We are also performing chemical screens using sensitized C. elegans genetic backgrounds to identify molecules that specifically interact with targeted pathways. In parallel, we screened a library of 300 uncharacterized Bacillus thuringiensis (Bt) strains (isolated by Mireille Kallassy – USJ, Lebanon). Bt is a spore-forming bacterium that synthesizes crystal inclusions, some of which are toxic against insects (used as bioinsecticides), nematodes and cancer cells. These crystal proteins are safe to humans, biodegradable, and constitute a promising alternative to chemical anthelmintics. We found 95 Bt strains that hinder the development of C. elegans or P. pacificus and are analyzing these to characterize new virulence factors and mechanisms of action.