Gene function prediction from synthetic lethality networks via ranking on demand.

MOTIVATION: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. RESULTS: In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.

The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose.

Circadian clocks are 24-h timing devices that phase cellular responses; coordinate growth, physiology, and metabolism; and anticipate the day-night cycle. Here we report sensitivity of the Arabidopsis thaliana circadian oscillator to sucrose, providing evidence that plant metabolism can regulate circadian function. We found that the Arabidopsis circadian system is particularly sensitive to sucrose in the dark. These data suggest that there is a feedback between the molecular components that comprise the circadian oscillator and plant metabolism, with the circadian clock both regulating and being regulated by metabolism. We used also simulations within a three-loop mathematical model of the Arabidopsis circadian oscillator to identify components of the circadian clock sensitive to sucrose. The mathematical studies identified GIGANTEA (GI) as being associated with sucrose sensing. Experimental validation of this prediction demonstrated that GI is required for the full response of the circadian clock to sucrose. We demonstrate that GI acts as part of the sucrose-signaling network and propose this role permits metabolic input into circadian timing in Arabidopsis.

Surface roughness noise prediction for silent aircraft experimental design SAX-40

Surface roughness noise is a potentially important contributor to airframe noise. In this paper, noise assessment due to surface roughness is performed for a conceptual Silent Aircraft design SAX-40 by means of a prediction model developed in previous theoretical work and validated experimentally. Estimates of three idealized test cases show that surface roughness could produce a significant noise level above that due to the trailing edge at high frequencies. Roughness height and roughness density are the two most significant parameters influencing surface roughness noise, with roughness height having the dominant effect. The ratio of roughness height to boundary-layer thickness is the relevant non-dimensional parameter and this decreases in the streamwise direction. The candidate surface roughness is selected for SAX-40 to meet an aggressive noise target and keep surface roughness noise at a negligible level. Copyright © 2008 by Yu Liu and Ann P. Dowling.