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.

Fecundity, egg deposition, and mortality of market squid (Lolilgo opalescens)

Loligo opalescens live less than a year and die after a short spawning period before all oocytes are expended. Potential fecundity (EP), the standing stock of all oocytes just before the onset of spawning, increased with dorsal mantle length (L), where EP = 29.8L. For the average female squid (L of 129 mm), EP was 3844 oocytes. During the spawning period, no oogonia were produced; therefore the standing stock of oocytes declined as they were ovulated. This decline in oocytes was correlated with a decline in mantle condition and an increase in the size of the smallest oocyte in the ovary. Close agreement between the decline in estimated body weight and standing stock of oocytes during the spawning period indicated that maturation and spawning of eggs could largely, if not entirely, be supported by the conversion of energy reserves in tissue. Loligo opalescens, newly recruited to the spawning population, ovulated about 36% of their potential fecundity during their first spawning day and fewer ova were released in subsequent days. Loligo opalescens do not spawn all of their oocytes; a small percentage of the spawning population may live long enough to spawn 78% of their potential fecundity. Loligo opalescens are taken in a spawning grounds fishery off California, where nearly all of the catch are mature spawning adults. Thirty-three percent of the potential fecundity of L. opalescens was deposited before they were taken by the fishery (December 1998−99). This observation led to the development of a management strategy based on monitoring the escapement of eggs from the fishery. The strategy requires estimation of the fecundity realized by the average squid in the population which is a function of egg deposition and mortality rates. A model indicated that the daily total mortality rate on the spawning ground may be about 0.45 and that the average adult may live only 1.67 days after spawning begins. The rate at which eggs escape the fishery was modeled and the sensitivity of changing daily rates of fishing mortality, natural mortality, and egg deposition was examined. A rapid method for monitoring the fecundity of the L. opalescens catch was developed.

Seasonal egg production of whitemouth croaker (Micropogonias furnieri) in the Río de la Plata estuary, Argentina-Uruguay

The reproductive biology of the whitemouth croaker (Micropogonias furnieri) inhabiting the estuarine waters of the Río de la Plata (Argentina-Uruguay) was studied by using histological analysis of the ovaries. Samples were collected during the spawning peak and the end of two breeding seasons (November 1995–Feb-ruary 1996 and November 1997–March 1998). Micropogonias furnieri is a multiple spawner with indeterminate annual fecundity. Spawning frequency, determined by using the percentage of females with postovulatory follicles, was about 31% in November 1995 and 25% in February 1996. At these frequencies, a female on average spawned a new batch of eggs every 3–4 days during the spawning season. Batch fecundity was fitted to a power function of length and a linear function of ovary-free female weight. The number of hydrated oocytes decreased at the end of the breeding season, coinciding with an increase of atresia. Annual egg production for a 40-cm-TL female was estimated to be between 3,300,000 and 7,300,000 eggs. In addition to the seasonal decrease in fecundity and spawning activity, a decline in egg size and weight toward the end of the breeding season was also observed.

Studies on the biochemical composition of some freshwater fishes. Pt. 3. Ovary

Biochemical composition of the spent ovaries of 23 different species of freshwater fishes showed a much lower value for protein and fat with higher moisture content than those of the ripe eggs, suggesting an inverse relationship between fat and moisture. Ovaries during the recovering phase showed fairly high values of phosphorus, but lower than those for the ripe eggs. Higher values of calcium and iron in spent ovaries than those in ripe eggs probably suggest that there is a greater requirement of calcium and iron during the spent phase of the gonads.