The ‘World Prodigy’ oil spill in Narragansett Bay,Rhode Island: acute effects on macrobenthic crustacean populations

On June 26,1989, the tanker World Prodigy ran aground just outside the mouth of the West Passage of Narragansett Bay, Rhode Island, USA. About 922 metric tons of No. 2 fuel oil were released into the water and drifted over a total area of about 120 sq miles. Three days after the spill only a small fraction of the oil remained.The effects on macrobenthic crustaceans within the first five weeks after the spill were studied at five stations with a varying degree of oil exposure, including one control site never reached by oil from the spill. Significant differencies between these stations were noted for total amphipod abundance, the amphipod genus Ampelisca and ostracods (retained on a 0.3 mm mesh), but not for amphipods of the genus Corophium. At the most heavily impacted station (23 µg oil g^–1 sediment dry weight), the total amphipod abundance, dominated by Ampelisca verrilli, decreased by 86% within the first two weeks after the spill. Decreases in total amphipod abundance significantly larger than at the control site were noted also at two other stations, one of which with only trace amounts of oil detected in the sediment. The amphipod populations at these sites were dominated by juvenile specimens.These findings confirm the extreme sensitivity to oil pollution of amphipods and ostracods, noted in earlier field and experimental studies.     

Polyamine-containing etoposide derivatives as poisons of human type II topoisomerases: Differential effects on topoisomerase IIα and IIβ

Etoposide is an anticancer drug that acts by inducing topoisomerase II-mediated DNA cleavage. Despite its wide use, etoposide is associated with some very serious side-effects including the development of treatment-related acute myelogenous leukemias. Etoposide targets both human topoisomerase IIα and IIβ. However, the contributions of the two enzyme isoforms to the therapeutic vs. leukemogenic properties of the drug are unclear. In order to develop an etoposide-based drug with specificity for cancer cells that express an active polyamine transport system, the sugar moiety of the drug has been replaced with a polyamine tail. To analyze the effects of this substitution on the specificity of hybrid molecules toward the two enzyme isoforms, we analyzed the activity of a series of etoposide-polyamine hybrids toward human topoisomerase IIα and IIβ. All of the compounds displayed an ability to induce enzyme-mediated DNA cleavage that was comparable to or higher than that of etoposide. Relative to the parent drug, the hybrid compounds displayed substantially higher activity toward topoisomerase IIβ than IIα. Modeling studies suggest that the enhanced specificity may result from interactions with Gln778 in topoisomerase IIβ. The corresponding residue in the α isoform is a methionine.     

Inferring gene regulatory networks from asynchronous microarray data with AIRnet

Background

Modern approaches to treating genetic disorders, cancers and even epidemics rely on a detailed understanding of the underlying gene signaling network. Previous work has used time series microarray data to infer gene signaling networks given a large number of accurate time series samples. Microarray data available for many biological experiments is limited to a small number of arrays with little or no time series guarantees. When several samples are averaged to examine differences in mean value between a diseased and normal state, information from individual samples that could indicate a gene relationship can be lost.

Results

Asynchronous Inference of Regulatory Networks (AIRnet) provides gene signaling network inference using more practical assumptions about the microarray data. By learning correlation patterns for the changes in microarray values from all pairs of samples, accurate network reconstructions can be performed with data that is normally available in microarray experiments.

Conclusions

By focussing on the changes between microarray samples, instead of absolute values, increased information can be gleaned from expression data.

     

NUTRIENTS AND THE PRODUCTIVITY OF ESTUARINE AND COASTAL MARINE ECOSYSTEMS

SUMMARY

Recent research on estuarine and coastal marine systems has revealed two particularly interesting things about nutrients and productivity. First is the observation that these areas are among the most intensively fertilized environments on earth. Second is the common finding that much of the characteristically high primary productivity of these shallow waters is supported by nutrients released or recycled by pelagic and benthic microheterotrophs. Since nutrient inputs to coastal areas have probably been increasing and are likely to continue to do so, it is particularly important to understand the relationship between nutrient loading and nutrient cycling and the extent to which their interactions may set the levels of primary and secondary production in coastal systems.

That some direct relationship exists between the input of nutrients and the productivity of higher trophic levels has been a principle of marine ecology since the turn of the century. It is surprisingly difficult, however, to find quantitative evidence showing that estuaries, lagoons, or other coastal waters respond to eutrophication by producing a larger biomass of animals. Part of this difficulty arises because the amount of nitrogen or phosphorus incorporated in animal tissue is a very small term in the total nutrient budget of an estuary, and the accuracy and precision of ecological field measurements may not be adequate to the task. In addition, the response of natural systems to nutrient enrichment is compounded by changes in climate, hydrography, harvesting effort and technology, and pollution.

Attempts to avoid some of these problems by carrying out controlled nutrient addition experiments in the field or with mesocosms have been much rarer in marine ecology than in limnology. The results that are available for such studies seem to suggest that there is a modest enhancement of primary production with nutrient addition, but that most of this extra organic matter is rapidly consumed, presumably by microheterotrophs. In other words, as nutrient inputs rise, so does the rate of nutrient recycling. Only a small fraction of the added nutrients appears as an increment in the production of higher trophic levels.     

Mass and metabolism of a mussel bed

Summary A mussel bed dominated by Mytilus edulis contained large concentrations of living consumer biomass, with over 14 kg dry weight/m² distributed among eleven species. An additional 14.4 kg dry weight/m² was present as empty shell fragments that contributed to community structure. Field measurements of community respiration for this dense animal system showed a roughly hyperbolic response to increasing current speed. In still water, oxygen uptake was 0.2g O₂/m²/hr while in currents over 0.1 m/sec it quickly rose to about 2.7 g O₂/m²/hr.This research was supported by a grant to the University of Rhode Island by the Office of Sea Grant Programs.     

Phytoplankton species and abundance in response to eutrophication in coastal marine mesocosms

In a mesocosm nutrient enrichment experiment the species (orcategories) and abundances of diatoms, dinoflagellates, flagellates,monads and ciliates were identified and counted over a 16-monthperiod. Diatoms and ciliates increased with increasing nutrienttreatment while monads and flagellates, <10 µm in size,did not. By contrast, in the field diatoms sometimes appearedto decrease while small phytoplankton µ10 µm appearedto increase under eutrophic conditions. In the experiment, insome instances, grazing controlled abundances to low levelsin nutrient-enriched treatments. Self-shading by phytoplanktonlimited upper levels of abundance when nutrients were excessive.While nuisance species were occasionally present in variousnutrient treatments, the intensity and frequency of their presencedid not tend to increase with nutrient treatment. Generallyspecies (or categories) did not appear to change with nutrienttreatment.     

Multivariate analysis of experimental marine ecosystems

Twelve replicate 150-l laboratory microcosms were developed using whole water samples and natural benthic communities from Narragansett Bay, Rhode Island (USA). The microcosms were scaled to the bay in terms of salinity, temperature, light input, volume pelagic community to area of benthic community, density of macrofauna, turbulent mixing, and flushing time. The microcosms were self maintaining during a six month study period with over 35 species of phytoplankton and 30 species of macro-invertebrates. Some 25 species of meroplankton entered the microcosms and sucessfully colonized the benthic communities. Zooplankton were present in all life stages. After an initial study of replication among the 12 tanks, the microcosms were perturbed with 3 levels of treated urban sewage for a three month period. Three microcosms were maintained at each level with 3 tanks remaining as controls. At the end of 3 months, the sewage input was terminated and the response of the systems was followed for an additional 2 months. Both time series data and multivariate statistical analysis of over 10 different parameters indicated that the replication of the microcosms was adequate to show the effects of experimental treatments. Control microcosms were generally within the range of variation expected in Narragansett Bay. Moreover, the results suggested that the microcosms responded to the gradient of sewage input in a manner similar to that of the bay. During the two month period after the sewage was discontinued, all of the microcosms became increasingly similar, though the tanks that had been subjected to higher levels of sewage remained distinct. It was apparent throughout the study that comparisons of microcosms and natural systems must account for the large variation characteristic of each. For this, and other reasons, multivariate statistical techniques appear to provide a powerful tool for experimental ecosystem analysis.     

The importance of physical and biotic scaling to the experimental simulation of a coastal marine ecosystem

A marine microcosm, consisting of a pelagic phase interacting with a benthic phase, is described. Variations in water turnover, turbulence, incident radiation and ratio of pelagic volume to benthic surface area are shown to have significant effects on the behavior of these microcosms. It is argued that the inclusion and accurate simulation of appropriate levels of these variables is important in microcosm studies designed to study the dynamics of natural systems.