Meeting highlights: genome informatics

We bring you the highlights of the second Joint Cold Spring Harbor Laboratory and Wellcome Trust 'Genome Informatics' Conference, organized by Ewan Birney, Suzanna Lewis and Lincoln Stein. There were sessions on in silico data discovery, comparative genomics, annotation pipelines, functional genomics and integrative biology. The conference included a keynote address by Sydney Brenner, who was awarded the 2002 Nobel Prize in Physiology or Medicine (jointly with John Sulston and H. Robert Horvitz) a month later.     

Seasonal cycles of zooplankton from San Francisco Bay

The two estuarine systems composing San Francisco Bay have distinct zooplankton communities and seasonal population dynamics. In the South Bay, a shallow lagoon-type estuary, the copepods Acartia spp. and Oithona davisae dominate. As in estuaries along the northeast coast of the U.S., there is a seasonal succession involving the replacement of a cold-season Acartia species (A. clausi s.l.) by a warm-season species (A. californiensis), presumably resulting from the differential production and hatching of dormant eggs. Oithona davisae is most abundant during the fall. Copepods of northern San Francisco Bay, a partially-mixed estuary of the Sacramento-San Joaquin Rivers, organize into discrete populations according to salinity distribution: Sinocalanus doerrii (a recently introduced species) at the riverine boundary, Eurytemora affinis in the oligohaline mixing zone, Acartia spp. in polyhaline waters (18–30\%), and neritic species (e.g., Paracalanus parvus) at the seaward boundary. Sinocalanus doerrii and E. affinis are present year-round. Acartia clausi s.l. is present almost year-round in the northern reach, and A. californiensis occurs only briefly there in summer-fall. The difference in succession of Acartia species between the two regions of San Francisco Bay may reflect differences in the seasonal temperature cycle (the South Bay warms earlier), and the perennial transport of A. clausi s.l. into the northern reach from the seaward boundary by nontidal advection.Large numbers (>10⁶ m^–3) of net microzooplankton (>64 µm), in cluding the rotifer Synchaeta sp. and three species of tintinnid ciliates, occur in the South Bay and in the seaward northern reach where salinity exceeds about 5–10 Maximum densities of these microzooplankton are associated with high concentrations of chlorophyll. Meroplankton (of gastropods, bivalves, barnacles, and polychaetes) constitute a large fraction of zooplankton biomass in the South Bay during winter-spring and in the northern reach during summer-fall.Seasonal cycles of zooplankton abundance appear to be constant among years (1978–1981) and are similar in the deep (>10 m) channels and lateral shoals (<3 m). The seasonal zooplankton community dynamics are discussed in relation to: (1) river discharge which alters salinity distribution and residence time of plankton; (2) temperature which induces production and hatching of dormant copepod eggs; (3) coastal hydrography which brings neritic copepods of different zoogeographic affinities into the bay; and (4) seasonal cycles of phytoplankton.     

HUPO Publications Committee Meeting: 21 April 2006, San Francisco, CA, USA

This meeting was convened with the aim of bringing together representatives from scientific journals, granting authorities, software and instrumentation manufacturers, data producers and database providers to discuss the implementation and adoption of the HUPO-PSI data standards and how these can be best used to support the publication and dissemination of proteomics data. The current status of data formats and reporting requirements was reviewed and the attendees agreed that the use of data standards was essential as the field of proteomics grows and matures.