Changes in the oceanic northeast Pacific plankton populations; what may happen in a warmer ocean

The Continuous Plankton Recorder has been sampling the northeast Pacific on a routine basis since 2000. Although this is a relatively short time series still, climate variability within that time has caused noticeable related changes in the plankton. The earlier part of the time series followed the 1999 La Nina and conditions were cool, but conditions between 2003 and 2005 were anomalously warm. Oceanic zooplankton have responded to this warming in several ways that are discernible in CPR data. The seasonal cycle of mesozooplankton biomass in the eastern Gulf of Alaska has shifted earlier in the spring by a few weeks (sampling resolution is too coarse to be more accurate). The copepod Neocalanus plumchruslflemingeri is largely responsible as it makes up a high proportion of the spring surface biomass and stage-based determinations have shown an earlier maximum in warmer years across much of the northeast Pacific, spanning nearly 20 degrees of latitude. Summer copepod populations are more diverse than in spring, although lower in biomass. The northwards extension of southern taxa in the summer correlates with surface temperature and in warmer years southern taxa are found further north than in cooler years. These findings support the importance of monitoring the open ocean particularly as it is an important foraging ground for large fish, birds and mammals. Higher trophic levels may time their reproduction or migration to coincide with the abundance of particular prey which may be of a different composition and/or lower abundance at a particular time in warmer conditions.

Spatial variability of the plankton trophic interaction in the North Sea: a new feature after the early 1970s

Traditionally, marine ecosystem structure was thought to be bottom-up controlled. In recent years, a number of studies have highlighted the importance of top-down regulation. Evidence is accumulating that the type of trophic forcing varies temporally and spatially, and an integrated view – considering the interplay of both types of control – is emerging. Correlations between time series spanning several decades of the abundances of adjacent trophic levels are conventionally used to assess the type of control: bottom-up if positive or top-down if this is negative. This approach implies averaging periods which might show time-varying dynamics and therefore can hide part of this temporal variability. Using spatially referenced plankton information extracted from the Continuous Plankton Recorder, this study addresses the potential dynamic character of the trophic structure at the planktonic level in the North Sea by assessing its variation over both temporal and spatial scales. Our results show that until the early-1970s a bottom-up control characterized the base of the food web across the whole North Sea, with diatoms having a positive and homogeneous effect on zooplankton filter-feeders. Afterwards, different regional trophic dynamics were observed, in particular a negative relationship between total phytoplankton and zooplankton was detected off the west coast of Norway and the Skagerrak as opposed to a positive one in the southern reaches. Our results suggest that after the early 1970s diatoms remained the main food source for zooplankton filter-feeders east of Orkney–Shetland and off Scotland, while in the east, from the Norwegian Trench to the German Bight, filter-feeders were mainly sustained by dinoflagellates.

Biodiversity as a dynamic variable in the Gulf of Maine continuous plankton recorder transect

Studies relating biodiversity to ecosystem processes typically do not take into account changes in biodiversity through time. Marine systems are highly dynamic, with biodiversity changing at diel, seasonal and inter-decadal timescales. We examined the dynamics of biodiversity in the Gulf of Maine pelagic zooplankton community. Taxonomic data came from the Gulf of Maine continuous plankton recorder (CPR) transect, spanning the years 1961–2006. The CPR transect also contains coincident information on temperature and phytoplankton biomass (measured by the phytoplankton color index). Taxonomic richness varied at all timescales considered. The relationships between temperature and richness, and between phytoplankton and richness, also depended on temporal scale. The temperature–richness relationship was monotonic at the multi-decadal scale, and tended to be hump-shaped at finer scales; the productivity–richness relationship was hump-shaped at the multi-decadal scale, and tended to be monotonic at finer scales. Seasonal biodiversity dynamics were linked to temperature; inter-decadal biodiversity dynamics were linked to phytoplankton.

Optimal foraging strategies: Lévy walks balance searching and patch exploitation under a very broad range of conditions

While evidence for optimal random search patterns, known as Lévy walks, in empirical movement data is mounting for a growing list of taxa spanning motile cells to humans, there is still much debate concerning the theoretical generality of Lévy walk optimisation. Here, using a new and robust simulation environment, we investigate in the most detailed study to date (24×10(6) simulations) the foraging and search efficiencies of 2-D Lévy walks with a range of exponents, target resource distributions and several competing models. We find strong and comprehensive support for the predictions of the Lévy flight foraging hypothesis and in particular for the optimality of inverse square distributions of move step-lengths across a much broader range of resource densities and distributions than previously realised. Further support for the evolutionary advantage of Lévy walk movement patterns is provided by an investigation into the 'feast and famine' effect, with Lévy foragers in heterogeneous environments experiencing fewer long 'famines' than other types of searchers. Therefore overall, optimal Lévy foraging results in more predictable resources in unpredictable environments.

A new approach for objective identification of turns and steps in organism movement data relevant to random walk modelling

1. A first step in the analysis of complex movement data often involves discretisation of the path into a series of step-lengths and turns, for example in the analysis of specialised random walks, such as Lévy flights. However, the identification of turning points, and therefore step-lengths, in a tortuous path is dependent on ad-hoc parameter choices. Consequently, studies testing for movement patterns in these data, such as Lévy flights, have generated debate. However, studies focusing on one-dimensional (1D) data, as in the vertical displacements of marine pelagic predators, where turning points can be identified unambiguously have provided strong support for Lévy flight movement patterns. 2. Here, we investigate how step-length distributions in 3D movement patterns would be interpreted by tags recording in 1D (i.e. depth) and demonstrate the dimensional symmetry previously shown mathematically for Lévy-flight movements. We test the veracity of this symmetry by simulating several measurement errors common in empirical datasets and find Lévy patterns and exponents to be robust to low-quality movement data. 3. We then consider exponential and composite Brownian random walks and show that these also project into 1D with sufficient symmetry to be clearly identifiable as such. 4. By extending the symmetry paradigm, we propose a new methodology for step-length identification in 2D or 3D movement data. The methodology is successfully demonstrated in a re-analysis of wandering albatross Global Positioning System (GPS) location data previously analysed using a complex methodology to determine bird-landing locations as turning points in a Lévy walk. For this high-resolution GPS data, we show that there is strong evidence for albatross foraging patterns approximated by truncated Lévy flights spanning over 3·5 orders of magnitude. 5. Our simple methodology and freely available software can be used with any 2D or 3D movement data at any scale or resolution and are robust to common empirical measurement errors. The method should find wide applicability in the field of movement ecology spanning the study of motile cells to humans.

Developments since 2005 in understanding potential environmental impacts of CO2 leakage from geological storage

This paper reviews research into the potential environmental impacts of leakage from geological storage of CO2 since the publication of the IPCC Special Report on Carbon Dioxide Capture and Storage in 2005. Possible impacts are considered on onshore (including drinking water aquifers) and offshore ecosystems. The review does not consider direct impacts on man or other land animals from elevated atmospheric CO2 levels. Improvements in our understanding of the potential impacts have come directly from CO2 storage research but have also benefitted from studies of ocean acidification and other impacts on aquifers and onshore near surface ecosystems. Research has included observations at natural CO2 sites, laboratory and field experiments and modelling. Studies to date suggest that the impacts from many lower level fault- or well-related leakage scenarios are likely to be limited spatially and temporarily and recovery may be rapid. The effects are often ameliorated by mixing and dispersion of the leakage and by buffering and other reactions; potentially harmful elements have rarely breached drinking water guidelines. Larger releases, with potentially higher impact, would be possible from open wells or major pipeline leaks but these are of lower probability and should be easier and quicker to detect and remediate.

Recovery from TBT pollution in English Channel environments: A problem solved?

Following recognition of effects in the 1980s, tributyltin (TBT) has been monitored at sites in the English Channel to evaluate the prognosis for biota – spanning the introduction of restrictions on TBT use on small boats and the recent phase-out on the global fleet. We describe how persistence and impact of TBT in clams Scrobicularia plana has changed during this period in Southampton Water and Poole Harbour. TBT contamination (and loss) in water, sediment and clams reflects the abundance and type of vessel activity: half-times in sediment (up to 8y in Poole, 33y in Southampton) are longest near commercial shipping. Recovery of clam populations – slowest in TBT-contaminated deposits – provides a useful biological measure of legislative efficacy in estuaries. On rocky shores, recovery from imposex in Nucella lapillus is evident at many sites but, near ports, is prolonged by shipping impacts, including sediment legacy, for example, in the Fal.

Questioning the role of phenology shifts and trophic mismatching in a planktonic food web

In a warming climate, differential shifts in the seasonal timing of predators and prey have been suggested to lead to trophic ‘‘mismatches’’ that decouple primary, secondary and tertiary production. We tested this hypothesis using a 25-year time-series of weekly sampling at the Plymouth L4 site, comparing 57 plankton taxa spanning 4 trophic levels. During warm years, there was a weak tendency for earlier timings of spring taxa and later timings of autumn taxa. While this is in line with many previous findings, numerous exceptions existed and only a few taxa (e.g. Gyrodinium spp., Pseudocalanus elongatus, and Acartia clausi) showed consistent, strong evidence for temperature-related timing shifts, revealed by all 4 of the timing indices that we used. Also, the calculated offsets in timing i.e. ‘‘mismatches’’) between predator and prey were no greater in extreme warm or cold years than during more average years. Further, the magnitude of these offsets had no effect on the ‘‘success’’ of the predator, in terms of their annual mean abundance or egg production rates. Instead numerous other factors override, including: inter-annual variability in food quantity, high food baseline levels, turnover rates and prolonged seasonal availability, allowing extended periods of production. Furthermore many taxa, notably meroplankton, increased well before the spring bloom. While theoretically a chronic mismatch, this likely reflects trade-offs for example in predation avoidance. Various gelatinous taxa (Phaeocystis, Noctiluca, ctenophores, appendicularians, medusae) may have reduced these predation constraints, with variable, explosive population outbursts likely responding to improved conditions. The match–mismatch hypothesis may apply for highly seasonal, pulsed systems or specialist feeders, but we suggest that the concept is being over-extended to other marine systems where multiple factors compensate.

GeneGrid: Architecture, Implementation and Application

The emergence of Grid computing technology has opened up an unprecedented opportunity for biologists to share and access data, resources and tools in an integrated environment leading to a greater chance of knowledge discovery. GeneGrid is a Grid computing framework that seamlessly integrates a myriad of heterogeneous resources spanning multiple administrative domains and locations. It provides scientists an integrated environment for the streamlined access of a number of bioinformatics programs and databases through a simple and intuitive interface. It acts as a virtual bioinformatics laboratory by allowing scientists to create, execute and manage workflows that represent bioinformatics experiments. A number of cooperating Grid services interact in an orchestrated manner to provide this functionality. This paper gives insight into the details of the architecture, components and implementation of GeneGrid.

Calibration of the Radiocarbon Time Scale for the Southern Hemisphere: AD 1850-950

We have conducted a series of radiocarbon measurements on decadal samples of dendrochronologically dated wood from both hemispheres, spanning 1000 years (McCormac et al. 1998; Hogg et al. this issue). Using the data presented in Hogg et al., we show that during the period AD 950-1850 the 14C offset between the hemispheres is not constant, but varies periodically (~130 yr periodicity) with amplitudes varying between 1 and 10‰ (i.e. 8-80 yr), with a consequent effect on the 14C calibration of material from the Southern Hemisphere. A large increase in the offset occurs between AD 1245 and 1355. In this paper, we present a Southern Hemisphere high-precision calibration data set (SHCal02) that comprises measurements from New Zealand, Chile, and South Africa. This data, and a new value of 41 ± 14 yr for correction of the IntCal98 data for the period outside the range given here, is proposed for use in calibrating Southern Hemisphere 14C dates.

A strategy for designing inhibitors of alpha-synuclein aggregation and toxicity as a novel treatment for Parkinson's disease and related disorders.

Convergent biochemical and genetic evidence suggests that the formation of alpha-synuclein (alpha-syn) protein deposits is an important and, probably, seminal step in the development of Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). It has been reported that transgenic animals overexpressing human alpha-syn develop lesions similar to those found in the brain in PD, together with a progressive loss of dopaminergic cells and associated abnormalities of motor function. Inhibiting and/or reversing alpha-syn self-aggregation could, therefore, provide a novel approach to treating the underlying cause of these diseases. We synthesized a library of overlapping 7-mer peptides spanning the entire alpha-syn sequence, and identified amino acid residues 64-100 of alpha-syn as the binding region responsible for its self-association. Modified short peptides containing alpha-syn amino acid sequences from part of this binding region (residues 69-72), named alpha-syn inhibitors (ASI), were found to interact with full-length alpha-syn and block its assembly into both early oligomers and mature amyloid-like fibrils. We also developed a cell-permeable inhibitor of alpha-syn aggregation (ASID), using the polyarginine peptide delivery system. This ASID peptide was able to inhibit the DNA damage induced by Fe(II) in neuronal cells transfected with alpha-syn(A53T), a familial PD-associated mutation. ASI peptides without this delivery system did not reverse levels of Fe(II)-induced DNA damage. Furthermore, the ASID peptide increased (P

A novel diagnostic test detects a low frequency of the hemicentin Gln5345Arg variant among Northern Irish age related macular degeneration patients.

Purpose: Age related macular degeneration (AMD) is a common cause of severe vision loss. Identification of genes involved in AMD will facilitate early detection and ultimately help to identify pathways for treatment for this disorder. The A16,263G mutation in the HEMICENTIN-1 gene produces a non-conservative substitution of arginine for glutamine at codon 5345 which has been implicated in familial AMD. The aim of this study is to develop a rapid diagnostic assay for the detection of this mutation and to evaluate its frequency in a sample of AMD patients. Methods: A primer probe set was designed from exon 104 of the HEMICENTIN-1 gene to differentiate between mutant and wild type alleles. A region spanning the mutation was amplified by PCR using a LightCycler (Roche Diagnostic). The mutation was then detected by melt curve analysis of the hybrid formed between the PCR product and a specific fluorescent probe. The frequency of the mutation within the Northern Ireland population was evaluated by assaying 508 affected AMD patients, 25 possibly affected and 163 controls. Results: This assay clearly discriminates between the A16,263G mutant and wild type HEMICENTIN-1 alleles. The wild type sequence has a single base mismatch with the probe which decreases the stability of the hybrid, resulting in a lower TM (TM=51.27 °C) than that observed for the perfectly matched mutant allele (TM=59.9 °C). The mutant allele was detected in only one of the 696 subjects, an affected AMD patient. Conclusions: We describe a rapid assay for the genotyping of the Gln5345Arg mutation using real-time fluorescence PCR to facilitate rapid processing of samples through combined amplification and detection steps. These characteristics are suitable for a clinical setting where high throughput diagnostic procedures are required. The frequency of this mutation within the Northern Ireland population has been estimated at 0.2%, concurring with previous findings that this mutation is a rare variant associated with AMD. A rapid diagnostic assay will facilitate a reliable and convenient evaluation of the frequency of the Gln5345Arg mutation and its association with AMD within other populations.

The VLT-FLAMES survey of massive stars: Observations in the Galactic clusters NGC 3293, NGC 4755 and NGC 6611

We introduce a new survey of massive stars in the Galaxy and the Magellanic Clouds using the Fibre Large Array Multi- Element Spectrograph ( FLAMES) instrument at the Very Large Telescope ( VLT). Here we present observations of 269 Galactic stars with the FLAMES- Giraffe Spectrograph ( R similar or equal to 25 000), in fields centered on the open clusters NGC3293, NGC4755 and NGC6611. These data are supplemented by a further 50 targets observed with the Fibre- Fed Extended Range Optical Spectrograph ( FEROS, R = 48 000). Following a description of our scientific motivations and target selection criteria, the data reduction methods are described; of critical importance the FLAMES reduction pipeline is found to yield spectra that are in excellent agreement with less automated methods. Spectral classifications and radial velocity measurements are presented for each star, with particular attention paid to morphological peculiarities and evidence of binarity. These observations represent a significant increase in the known spectral content of NGC3293 and NGC4755, and will serve as standards against which our subsequent FLAMES observations in the Magellanic Clouds will be compared.

The WASP Project and the SuperWASP Cameras

The SuperWASP cameras are wide-field imaging systems at the Observatorio del Roque de los Muchachos on the island of La Palma in the Canary Islands, and at the Sutherland Station of the South African Astronomical Observatory. Each instrument has a field of view of some 482 deg2 with an angular scale of 13.7" pixel-1, and is capable of delivering photometry with accuracy better than 1% for objects having V~7.0-11.5. Lower quality data for objects brighter than V~15.0 are stored in the project archive. The systems, while designed to monitor fields with high cadence, are capable of surveying the entire visible sky every 40 minutes. Depending on the observational strategy, the data rate can be up to 100 Gbytes per night. We have produced a robust, largely automatic reduction pipeline and advanced archive, which are used to serve the data products to the consortium members. The main science aim of these systems is to search for bright transiting exoplanet systems suitable for spectroscopic follow-up observations. The first 6 month season of SuperWASP-North observations produced light curves of ~6.7 million objects with 12.9 billion data points.

Co-inheritance of two rare genodermatoses (Papillon Lefevre syndrome and Oculocutaneous Albinism Type 1) in two families

The co-occurrence of two rare recessive genetic conditions in apparently unrelated individuals or families is extremely rare. Two geographically distant and apparently unrelated families were identified in which individuals were simultaneously affected by two rare recessive mendelian syndromes, Papillon-Lefevre syndrome and type 1 oculocutaneous albinism. The families were tested for mutations in the causative genes, cathepsin C (CTSC) and tyrosinase (TYR), respectively, by direct sequencing. To assess the relationship of the two families, both families were tested for polymorphisms at eight microsatellite markers spanning both CTSC and TYR loci. Independent mutations (c.318-1G-->A and c.817G-->C/p.W272C) were identified in CTSC and TYR, respectively, that were shared by the affected individuals in both families. The two affected genes lie close together on chromosome bands 11q14.2-14.3, and studies with linked genetic markers suggested that the families shared a small chromosomal segment carrying both mutations that had been transmitted intact from a remote common ancestor. The co-occurrence of the two rare diseases in multiple families depends on their shared chromosomal location, but not on any shared pathogenic mechanism.