Registry of samples and environmental context from the Ocean Sampling Day 2014

The Ocean Sampling Day (OSD) is a simultaneous sampling campaign of the world's oceans which took place (for the first time) on the summer solstice (June 21st) in the year 2014. These cumulative samples, related in time, space and environmental parameters, provide insights into fundamental rules describing microbial diversity and function and contribute to the blue economy through the identification of novel, ocean-derived biotechnologies. We see OSD data as a reference data set for generations of experiments to follow in the coming decade. The present data set includes a description of each sample collected during the Ocean Sampling Day 2014 and provides contextual environmental data measured concurrently with the collection of water samples for genomic analyses.

The effect of flow speed and food size on the capture efficiency and feeding behaviour of the cold-water coral Lophelia pertusa

Acknowledgements The authors acknowledge L. Wicks and B. de Francisco for helping in coral sampling and coral care in the aquaria facilities at SAMS. Thanks to C. Campbell and the CCAP for kind support and help. Scientific party and crew on board the RVs Calanus and Seol Mara, as well as on board the RRS James Cook during the Changing Oceans cruise (JC_073) are greatly acknowledged. Thanks to colleagues at SAMS for their support during our stay at SAMS. We are in debt with A. Olariaga for his help modifying the cylindrical experimental chambers used in the experiments, and C.C. Suckling for assistance with the flume experiment. Many thanks go to G. Kazadinis for preparing the POM used in the feeding experiments. We also thank two anonymous reviewers and the editor for their constructive comments, which contribute to improve the manuscript. This work has been supported by the European Commission through two ASSEMBLE projects (grant agreement no. 227799) conducted in 2010 and 2011 at SAMS, as well as by the UK Ocean Acidification Research Programme's Benthic Consortium project (awards NE/H01747X/1 and NE/H017305/1) funded by NERC. [SS]

A first trial of retrospective collaboration for positional cloning in complex inheritance: Assay of the cytokine region on chromosome 5 by the Consortium on Asthma Genetics (COAG)

The central problem of complex inheritance is to map oligogenes for disease susceptibility, integrating linkage and association over samples that differ in several ways. Combination of evidence over multiple samples with 1,037 families supports loci contributing to asthma susceptibility in the cytokine region on 5q [maximum logarithm of odds (lod) = 2.61 near IL-4], but no evidence for atopy. The principal problems with retrospective collaboration on linkage appear to have been solved, providing far more information than a single study. A multipoint lod table evaluated at commonly agreed reference loci is required for both collaboration and metaanalysis, but variations in ascertainment, pedigree structure, phenotype definition, and marker selection are tolerated. These methods are invariant with statistical methods that increase the power of lods and are applicable to all diseases, motivating collaboration rather than competition. In contrast to linkage, positional cloning by allelic association has yet to be extended to multiple samples, a prerequisite for efficient combination with linkage and the greatest current challenge to genetic epidemiology.

What was natural in the coastal oceans?

Humans transformed Western Atlantic coastal marine ecosystems before modern ecological investigations began. Paleoecological, archeological, and historical reconstructions demonstrate incredible losses of large vertebrates and oysters from the entire Atlantic coast. Untold millions of large fishes, sharks, sea turtles, and manatees were removed from the Caribbean in the 17th to 19th centuries. Recent collapses of reef corals and seagrasses are due ultimately to losses of these large consumers as much as to more recent changes in climate, eutrophication, or outbreaks of disease. Overfishing in the 19th century reduced vast beds of oysters in Chesapeake Bay and other estuaries to a few percent of pristine abundances and promoted eutrophication. Mechanized harvesting of bottom fishes like cod set off a series of trophic cascades that eliminated kelp forests and then brought them back again as fishers fished their way down food webs to small invertebrates. Lastly, but most pervasively, mechanized harvesting of the entire continental shelf decimated large, long-lived fishes and destroyed three-dimensional habitats built up by sessile corals, bryozoans, and sponges. The universal pattern of losses demonstrates that no coastal ecosystem is pristine and few wild fisheries are sustainable along the entire Western Atlantic coast. Reconstructions of ecosystems lost only a century or two ago demonstrate attainable goals of establishing large and effective marine reserves if society is willing to pay the costs. Historical reconstructions provide a new scientific framework for manipulative experiments at the ecosystem scale to explore the feasibility and benefits of protection of our living coastal resources.

World Bathymetric Chart of the Oceans, 1899 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Bathymetrical chart of the oceans, showing the "deeps" according to Sir John Murray. It was published by the Royal Geographical Society in 1899. Scale [ca. 1:100,000,000]. The image inside the map neatline is georeferenced to the surface of the earth and fit to the 'World Gall Stereographic' projection with the central meridian at 20.00000 degrees west. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, shoreline features, and more. Relief shown by hypsometric tints. Depths shown by gradient tints. This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection and the Harvard University Library as part of the Open Collections Program at Harvard University project: Organizing Our World: Sponsored Exploration and Scientific Discovery in the Modern Age. Maps selected for the project correspond to various expeditions and represent a range of regions, originators, ground condition dates, scales, and purposes.

Signalling in malaria parasites. The MALSIG consortium

Depending on their developmental stage in the life cycle, malaria parasites develop within or outside host cells, and in extremely diverse contexts such as the vertebrate liver and blood circulation, or the insect midgut and hemocoel. Cellular and molecular mechanisms enabling the parasite to sense and respond to the intra- and the extra-cellular environments are therefore key elements for the proliferation and transmission of Plasmodium, and therefore are, from a public health perspective, strategic targets in the fight against this deadly disease. The MALSIG consortium, which was initiated in February 2009, was designed with the primary objective to integrate research ongoing in Europe and India on i) the properties of Plasmodium signalling molecules, and ii) developmental processes occurring at various points of the parasite life cycle. On one hand, functional studies of individual genes and their products in Plasmodium falciparum (and in the technically more manageable rodent model Plasmodium berghei) are providing information on parasite protein kinases and phosphatases, and of the molecules governing cyclic nucleotide metabolism and calcium signalling. On the other hand, cellular and molecular studies are elucidating key steps of parasite development such as merozoite invasion and egress in blood and liver parasite stages, control of DNA replication in asexual and sexual development, membrane dynamics and trafficking, production of gametocytes in the vertebrate host and further parasite development in the mosquito. This article, which synthetically reviews such signalling molecules and cellular processes, aims to provide a glimpse of the global frame in which the activities of the MALSIG consortium will develop over the next three years.

Neogene radiolarian datum levels in the equatorial Indian and Pacific Oceans

Fifty radiolarian events of early Pleistocene and Neogene age were identified in an E-W transect of equatorial DSDP sites, extending from the Gulf of Panama to the western Pacific and eastern Indian Oceans. Our objective was to document the degree of synchroneity or time-transgressiveness of stratigraphically-useful datum levels from this geologic time interval. We restricted our study to low latitudes within which morphological variations of individual taxa are minimal, the total assemblage diversity remains high, and stratigraphic continuity is well-documented by an independent set of criteria. Each of the five sites chosen (503, 573, 289/586, 214) was calibrated to an "absolute" time scale, using a multiple of planktonic foraminiferal, nannofossil, and diatom datum levels which have been independently correlated to the paleomagnetic polarity time scale in piston core material. With these correlations we have assigned "absolute" ages to each radiolarian event, with a precision of 0.1-0.2 m.y. and an accuracy of 0.2-0.4 m.y. On this basis we have classified each of the events as either: (a) synchronous (range of ages <0.4 m.y.); (b) time-transgressive (i.e., range of ages >1.0 m.y.); and (c) not resolvable (range of ages 0.4-1.0 m.y.). Our results show that, among the synchronous datum levels, a large majority (15 out of 19) are last occurrences. Among those events which are clearly time-transgressive, most are first appearances (10 out of 13). In many instances taxa appear to evolve first in the Indian Ocean, and subsequently in the western and eastern Pacific Ocean. This pattern is particularly unexpected in view of the strong east-to-west zonal flow in equatorial latitudes. Three of the time-transgressive events have been used to define zonal boundaries: the first appearances of Spongaster pentas, Diartus hughesi, and D. petterssoni. Our results suggest that biostratigraphic non-synchroneity may be substantial (i.e., greater than 1 m.y.) within a given latitudinal zone; one would expect this effect to be even more pronounced across oceanographic and climatic gradients. We anticipate that the extent of diachroneity may be comparable for diatom, foraminiferal, and nannofossil datum levels as well. If this proves true, global "time scales" may need to be re-formulated on the basis of a smaller number of demonstrably synchronous events.

Lithium and rubidium concentrations in waters of seas and oceans

Data on lithium, rubidium and cesium concentrations in waters of open seas and oceans are summarized. Average amounts of these elements in the World Ocean inferred from published data and those obtained by the author are as follows: Li - 0.18 mg/l, Rb - 0.12 mg/l and Cs - 0.004 mg/l. Rare alkaline elements in the oceans and open seas are distributed (like sodium and potassium) in accordance with salinity. The ability of lithium to become a constituent of clay minerals accounts for its relatively low concentration in sea water as compared with that of sodium and potassium. Compared to rubidium and cesium that have high absorption energy and low hydration energy, lithium relatively enriches sea water. Residence times of these elements in the ocean are: Na - 120 My, Li - 2.7 My, Rb - 2.3 My and Cs - 0.3 My.

Sedimentation rates calculated on surface sediment samples from different site of the Atlantic and Pacific Oceans (Table 1)

Radiocarbon ages on CaCO3 from deep-sea cores offer constraints on the nature of the CaCO3 dissolution process. The idea is that the toll taken by dissolution on grains within the core top bioturbation zone should be in proportion to their time of residence in this zone. If so, dissolution would shift the mass distribution in favor of younger grains, thereby reducing the mean radiocarbon age for the grain ensemble. We have searched in vain for evidence supporting the existence of such an age reduction. Instead, we find that for water depths of more than 4 km in the tropical Pacific the radiocarbon age increases with the extent of dissolution. We can find no satisfactory steady state explanation and are forced to conclude that this increase must be the result of chemical erosion. The idea is that during the Holocene the rate of dissolution of CaCO3 has exceeded the rain rate of CaCO3. In this circumstance, bioturbation exhumes CaCO3 from the underlying glacial sediment and mixes it with CaCO3 raining from the sea surface.