The role of research networks for science-policy collaboration in coastal areas

This paper reviews the approach taken by several UK coastal partnerships in developing research strategies and programmes. It reports on the status of these research initiatives and describes how the co-ordination and communication of scientific research have been approached through active partnerships with universities and the wider research community. Results of semi-structured interviews are followed by in-depth case studies of research networks on the Sefton Coast (focusing on coastal morphology) and the Severn Estuary (focusing on coastal change and climate change impacts). The results reveal the constraints and opportunities that exist in bringing together a variety of knowledge holders in the coastal zone. The paper identifies key elements of these initiatives and highlights lessons that can be applied to the development of other research initiatives in order to achieve science supported, ecosystem-based management.     

Trace element and molecular markers of organic carbon dynamics along a shelf–basin continuum in sediments of the western Arctic Ocean

Molecular organic biomarkers together with trace element composition were investigated in sediments east of Barrow Canyon in the western Arctic Ocean to determine sources and recycling of organic carbon in a continuum from the shelf to the basin. Algal biomarkers (polyunsaturated and short-chain saturated fatty acids, 24-methylcholesta-5,24(28)-dien-3β-ol, dinosterol) highlight the substantial contribution of organic matter from water column and sea-ice primary productivity in shelf environments, while redox markers such as acid volatile sulfide (AVS), Mn, and Re indicate intense metabolism of this material leading to sediment anoxia. Shelf sediments also receive considerable inputs from terrestrial organic carbon, with biomarker composition suggesting the presence of multiple pools of terrestrial organic matter segregated by age/lability or hydrodynamic sorting. Sedimentary metabolism was not as intense in slope sediments as on the shelf; however, sufficient labile organic matter is present to create suboxic and anoxic conditions, at least intermittently, as organic matter is focused towards the slope. Basin sediments also showed evidence for episodic delivery of labile organic carbon inputs despite the strong physical controls of water depth and sea-ice cover. Principal components analysis of the lipid biomarker data was used to estimate fractions of preserved recalcitrant (of terrestrial origin) and labile (of marine origin) organic matter in the sediments, with ranges of 12–79%, 14–45%, and 37–66% found for the shelf, slope, and basin cores, respectively. On average, the relative preserved terrestrial organic matter in basin sediments was 56%, suggesting exchange of organic carbon between nearshore and basin environments in the western Arctic.     

A wave averaged energy equation: Comment on “global estimates of wind energy input to subinertial motions in the Ekman-Stokes layer” by Bin Liu,Kejian Wu and Changlong Guan

In a recent paper, Liu et al. (2007) formulate an expression for how surface gravity waves modify the Ekman layer energy budget. They then diagnose the effect in the world oceans using available data. This comment addresses the formulation of the energy equation that is fundamental to their study.     

Long-term bottom water warming in the north Ross Sea

We measured potential temperature, salinity, and dissolved oxygen profiles from the surface to the bottom at two locations in the north Ross Sea (65.2°S, 174.2°E and 67.2°S, 172.7°W) in December 2004. Comparison of our data with previous results from the same region reveals an increase in potential temperature and decreases in salinity and dissolved oxygen concentration in the bottom layer (deeper than 3000 m) over the past four decades. The changes were significantly different from the analytical precisions. Detailed investigation of the temperature, salinity, dissolved oxygen and σ ₃ value distributions and the bottom water flow in the north Ross Sea suggests a long-term change in water mass mixing balance. That is to say, it is speculated that the influence of cool, saline, high-oxygen bottom water (high-salinity Ross Sea Bottom Water) formed in the southwestern Ross Sea has possibly been decreased, while the influences of relatively warmer and fresher bottom water (low-salinity Ross Sea Bottom Water) and the Adélie Land Bottom Water coming from the Australia-Antarctic Basin have increased. The possible impact of global warming on ocean circulation needs much more investigation.     

Differential reproductive strategies of two bivalves in the Dutch Wadden Sea

Cerastoderma edule and Mya arenaria are two common bivalve species in European waters. Longevity and maximum size are much greater in the latter species. Because comparison of species life-history strategies states that a long life span (i.e. high annual survival) generally goes with lower fecundity, we hypothesise that reproductive output would be lower in M. arenaria than in C. edule. In the present paper, we studied the reproductive strategies of these two species in an intertidal and a subtidal area of the western Dutch Wadden Sea, by following seasonal changes in absolute and relative weights of somatic and gonadal tissues in these bivalves. Starting of spawning was similar in the two species, around May, except for intertidal M. arenaria, which initiated spawning in August. Individual energy investment in reproduction was similar for the two species but, unlike M. arenaria, C. edule spawned completely, releasing all energy of gonadal mass in the form of gametes. Mya arenaria used the gonad not only for reproduction but also for storage. In the intertidal area, we found a trade-off between longevity and reproduction, i.e. maximum reproductive output (expressed as a proportion of body mass) was higher in C. edule than in M. arenaria. However, since body size is larger and life span longer in M. arenaria than in C. edule, mean lifetime reproductive output per individual must be higher in the first than in the latter. Based on the differences in reproductive strategies of these two species, we hypothesise that the negative effects of warming climate on bivalve population dynamics in the Wadden Sea will be stronger in C. edule than in M. arenaria.     

MedFlux: Investigations of particle flux in the Twilight Zone

The MedFlux project was devised to determine and model relationships between organic matter and mineral ballasts of sinking particulate matter in the ocean. Specifically we investigated the ballast ratio hypothesis, tested various commonly used sampling and modeling techniques, and developed new technologies that would allow better characterization of particle biogeochemistry. Here we describe the rationale for the project, the biogeochemical provenance of the DYFAMED site, the international support structure, and highlights from the papers published here. Additional MedFlux papers can be accessed at the MedFlux web site (http://msrc.sunysb.edu/MedFlux/).     

Wave breaking on turbulent energy budget in the ocean surface mixed layer

As an important physical process at the air-sea interface, wave movement and breaking have a significant effect on the ocean surface mixed layer （OSML）. When breaking waves occur at the ocean surface, turbulent kinetic energy （TKE） is input downwards, and a sublayer is formed near the surface and turbulence vertical mixing is intensively enhanced. A one-dimensional ocean model including the Mellor-Yamada level 2.5 turbulence closure equations was employed in our research on variations in turbulent energy budget within OSML. The influence of wave breaking could be introduced into the model by modifying an existing surface boundary condition of the TKE equation and specifying its input. The vertical diffusion and dissipation of TKE were effectively enhanced in the sublayer when wave breaking was considered. Turbulent energy dissipated in the sublayer was about 92.0% of the total depth-integrated dissipated TKE, which is twice higher than that of non-wave breaking. The shear production of TKE decreased by 3.5% because the mean flow fields tended to be uniform due to wave-enhanced turbulent mixing. As a result, a new local equilibrium between diffusion and dissipation of TKE was reached in the wave-enhanced layer. Below the sublayer, the local equilibrium between shear production and dissipation of TKE agreed with the conclusion drawn from the classical law-of-the-wall （Craig and Banner, 1994）.     

Cloning and sequence analysis of a full-length cDNA of <Emphasis Type="Italic">SmPP1cb</Emphasis> encoding turbot protein phosphatase 1 beta catalytic subunit

Reversible protein phosphorylation, catalyzed by protein kinases and phosphatases, is an important and versatile mechanism by which eukaryotic cells regulate almost all the signaling processes. Protein phosphatase 1 （PP1） is the first and well-characterized member of the protein serine/threonine phosphatase family. In the present study, a full-length cDNA encoding the beta isoform of the catalytic subunit of protein phosphatase l（PPlcb）, was for the first time isolated and sequenced from the skin tissue of flatfish turbot Scophthalmus maximus, designated SmPPlcb, by the rapid amplification of cDNA ends （RACE） technique. The cDNA sequence of SmPPlcb we obtained contains a 984 bp open reading frame （ORF）, flanked by a complete 39 bp 5＇ untranslated region and 462 bp 3＇ untranslated region. The ORF encodes a putative 327 amino acid protein, and the N-terminal section of this protein is highly acidic, Met-Ala-Glu-Gly-Glu-Leu-Asp-Val-Asp, a common feature for PP1 catalytic subunit but absent in protein phosphatase 2B （PP2B）. And its calculated molecular mass is 37 193 Da and pI 5.8. Sequence analysis indicated that, SmPPlcb is extremely conserved in both amino acid and nucleotide acid levels compared with the PPlcb of other vertebrates and invertebrates, and its Kozak motif contained in the 5＇UTR around ATG start codon is GXXAXXGXXATGG, which is different from mammalian in two positions A6 and G3, indicating the possibility of different initiation of translation in turbot, and also the 3＇UTR of SmPPlcb is highly diverse in the sequence similarity and length compared with other animals, especially zebraf＇lsh. The cloning and sequencing of SmPPlcb gene lays a good foundation for the future work on the biological functions of PP1 in the flatfish turbot.     

Sequence analysis and quantitative detection of Norwalk-like viruses in cultured oysters of China

We isolated 4 Norwalk-like viruses (NLVs) contaminated oysters from 33 Chinese oysters collected from local commer-cial sources of Shandong Province. After amplification of the RNA-dependent RNA polymerase (RdRp) region of NLVs genomes with RT-PCR, the open reading frame 1 (ORF1) of the RdRp was sequenced and subjected to multiple-sequence alignment. The re-suits showed that NLVs in the four isolates belong to genogroup Ⅱ. The sequence comparison showed that the similarity between four Chinese oyster isolates were higher than 99.0%, which indicated that NLVs prevalent in close areas have high homogeneity in genome sequences. In addition, the most conserved sequences between diverse NLVs were used to design primers and TaqMan probes, then the real-time quantitative PCR assay was performed. According to the standard curve of GII NLVs, the original amounts (copies) of NLVs in positive patient's fecal isolate, positive Japanese oyster isolate, and the Chinese oyster isolate were 8.9×108, 1.25×108 and 4.7×101 respectively. The detecting limit of NLVs was 1×101 copies. This study will be helpful for routine diagnosis of NLVs pathogens in foods and thus for avoiding food poisoning in the future.