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 distribution of larval fishes of the Charleston Gyre Region off the southeastern United States in winter shaped by mesoscale, cyclonic eddies

Serial, cyclonic, mesoscale eddies arise just north of the Charleston Bump, a topographical rise on the continental slope and Blake Plateau, and characterize the U.S. outer shelf and upper slope in the region of the Charleston Gyre. This region was transected during the winters of 2000, 2001, and 2002, and hydrographic data and larval fishes were collected. The hydrodynamics of the cyclonic eddies of the Charleston Gyre shape the distribution of larval fishes by mixing larvae from the outer continental shelf and the Gulf Stream and entraining them into the eddy circulation at the peripheral margins, the wrap-around filaments. Over all years and transects (those that intercepted eddies and those that did not), chlorophyll a concentrations, zooplankton displacement volumes, and larval fish concentrations were positively correlated. Chlorophyll a concentrations were highest in filaments that wrapped around eddies, and zooplankton displacement volumes were highest in the continental shelf–Gulf Stream–frontal mix. Overall, the concentration of all larval fishes declined from inshore to offshore with highest concentrations occurring over the outer shelf. Collections produced larvae from 91 fish families representing continental shelf and oceanic species. The larvae of shelf-spawned fishes—Atlantic Menhaden Brevoortia tyrannus, Round Herring Etrumeus teres, Spot Leiostomus xanthurus, and Atlantic Croaker Micropogonias undulatus—were most concentrated over the outer shelf and in the continental shelf–Gulf Stream–frontal mix. The larvae of ocean-spawned fishes—lanternfishes, bristlemouths, and lightfishes—were more evenly dispersed in low concentrations across the outer shelf and upper slope, the highest typically in the Gulf Stream and Sargasso Sea, except for lightfishes that were highest in the continental shelf–Gulf Stream–frontal mix. Detrended correspondence analysis rendered groups of larval fishes that corresponded with a gradient between the continental shelf and Gulf Stream and Sargasso Sea. Eddies propagate northeastward with a residence time on the outer shelf and upper slope of ∼1 month, the same duration as the larval period of most fishes. The pelagic habitat afforded by eddies and fronts of the Charleston Gyre region can be exploited as nursery areas for feeding and growth of larval fishes within the southeastern Atlantic continental shelf ecosystem of the U.S. Eddies, and the nursery habitat they provide, translocate larvae northeastward.

An evaluation of back-calculation methodology using simulated otolith data

I simulated somatic growth and accompanying otolith growth using an individual-based bioenergetics model in order to examine the performance of several back-calculation methods. Four shapes of otolith radius-total length relations (OR-TL) were simulated. Ten different back-calculation equations, two different regression models of radius length, and two schemes of annulus selection were examined for a total of 20 different methods to estimate size at age from simulated data sets of length and annulus measurements. The accuracy of each of the twenty methods was evaluated by comparing the back-calculated length-at-age and the true length-at-age. The best back-calculation technique was directly related to how well the OR-TL model fitted. When the OR-TL was sigmoid shaped and all annuli were used, employing a least squares linear regression coupled with a log-transformed Lee back-calculation equation (y-intercept corrected) resulted in the least error; when only the last annulus was used, employing a direct proportionality back-calculation equation resulted in the least error. When the OR-TL was linear, employing a functional regression coupled with the Lee back-calculation equation resulted in the least error when all annuli were used, and also when only the last annulus was used. If the OR-TL was exponentially shaped, direct substitution into the fitted quadratic equation resulted in the least error when all annuli were used, and when only the last annulus was used. Finally, an asymptotically shaped OR-TL was best modeled by the individually corrected Weibull cumulative distribution function when all annuli were used, and when only the last annulus was used.