Field measurements of the fluid and sediment-dynamic environment of a benthic deposit feeder

Field measurements of flow and sediment transport at an intertidal site in False Bay, San Juan Island, Washington, U.S.A., revealed an environment dominated by wind wave-generated oscillatory flows and discrete sediment suspension events. Time series data showed that within a few tenths of a second, near-bottom suspended sediment concentrations can rise to 10 g l–1. These rapid erosion events are correlated with peak wave velocities and are followed by a more gradual (tens of seconds) decline in sediment concentration due to settling and advection. Large suspension events mixed detect able quantities of sediment to a height of 20 cm above the bottom. Flow and sediment transport rates are controlled by local weather and vary on time scales ranging from that of individual waves to that of atmospheric storm systems and seasonal changes in weather patterns. Advection of sediment can exceed individual deposit feeding rates by a factor of 103–104. An empirical relationship developed from weather records, together with previously published observations of detrital transport, suggests that sediment transport is rarely small enough in magnitude to be ignored as a source of food particles for surface deposit- and suspension-feeding spionid polychaetes like Pseudopolydora kempi japonica.

Linking Sediment Transport and Stratigraphy on the Continental Shelf

The goal of the shelf sediment dynamics component of STRATAFORM is to link sediment transport processes active on the continental shelfto the formation and preservation of event beds inshelf sediment deposits. An approach combiningshelf sediment-transport models with high-resolution measurements of water-column and bed properties over periods from several months to severalyears allows us to make quantitative estimates of bed modification caused by sediment resuspension during episodic transport events

Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1

Background: The entomopathogenic nematode Heterorhabditis bacteriophora and its symbiotic bacterium, Photorhabdus luminescens, are important biological control agents of insect pests. This nematode-bacterium-insect association represents an emerging tripartite model for research on mutualistic and parasitic symbioses. Elucidation of mechanisms underlying these biological processes may serve as a foundation for improving the biological control potential of the nematode-bacterium complex. This large-scale expressed sequence tag (EST) analysis effort enables gene discovery and development of microsatellite markers. These ESTs will also aid in the annotation of the upcoming complete genome sequence of H. bacteriophora. Results: A total of 31,485 high quality ESTs were generated from cDNA libraries of the adult H. bacteriophora TTO1 strain. Cluster analysis revealed the presence of 3,051 contigs and 7,835 singletons, representing 10,886 distinct EST sequences. About 72% of the distinct EST sequences had significant matches (E value < 1e-5) to proteins in GenBank's non-redundant (nr) and Wormpep190 databases. We have identified 12 ESTs corresponding to 8 genes potentially involved in RNA interference, 22 ESTs corresponding to 14 genes potentially involved in dauer-related processes, and 51 ESTs corresponding to 27 genes potentially involved in defense and stress responses. Comparison to ESTs and proteins of free-living nematodes led to the identification of 554 parasitic nematode-specific ESTs in H. bacteriophora, among which are those encoding F-box-like/WD-repeat protein theromacin, Bax inhibitor-1-like protein, and PAZ domain containing protein. Gene Ontology terms were assigned to 6,685 of the 10,886 ESTs. A total of 168 microsatellite loci were identified with primers designable for 141 loci. Conclusion: A total of 10,886 distinct EST sequences were identified from adult H. bacteriophora cDNA libraries. BLAST searches revealed ESTs potentially involved in parasitism, RNA interference, defense responses, stress responses, and dauer-related processes. The putative microsatellite markers identified in H. bacteriophora ESTs will enable genetic mapping and population genetic studies. These genomic resources provide the material base necessary for genome annotation, microarray development, and in-depth gene functional analysis