Analysis of protein networks in resting and collagen receptor (GPVI)-stimulated platelet sub-proteomes.

Proteomics approaches have made important contributions to the characterisation of platelet regulatory mechanisms. A common problem encountered with this method, however, is the masking of low-abundance (e.g. signalling) proteins in complex mixtures by highly abundant proteins. In this study, subcellular fractionation of washed human platelets either inactivated or stimulated with the glycoprotein (GP) VI collagen receptor agonist, collagen-related peptide, reduced the complexity of the platelet proteome. The majority of proteins identified by tandem mass spectrometry are involved in signalling. The effect of GPVI stimulation on levels of specific proteins in subcellular compartments was compared and analysed using in silico quantification, and protein associations were predicted using STRING (the search tool for recurring instances of neighbouring genes/proteins). Interestingly, we observed that some proteins that were previously unidentified in platelets including teneurin-1 and Van Gogh-like protein 1, translocated to the membrane upon GPVI stimulation. Newly identified proteins may be involved in GPVI signalling nodes of importance for haemostasis and thrombosis.

Regulation of platelet biology by platelet endothelial cell adhesion molecule-1.

Platelet endothelial cell adhesion molecule-1 (PECAM-1), an immunoreceptor tyrosine-based inhibitory motif containing receptor, plays diverse and apparently contradictory roles in regulating the response of platelets to stimuli; inhibiting platelet response to immunoreceptor tyrosine-based activation motif and G protein-coupled receptor signalling following stimulation with collagen, adenosine diphosphate, and thrombin, as well as enhancing integrin outside-in signalling. These dual, and opposing, roles suggest an important and complex role for PECAM-1 in orchestrating platelet response to vascular damage. Indeed, during thrombus formation, the influence of PECAM-1 on the multiple signalling pathways combines leading to a relatively large inhibitory effect on thrombus formation.

Eight-plex iTRAQ analysis of variant metastatic human prostate cancer cells identifies candidate biomarkers of progression: an exploratory study.

BACKGROUND: Due to the heterogeneity in the biological behavior of prostate cancer, biomarkers that can reliably distinguish indolent from aggressive disease are urgently needed to inform treatment choices. METHODS: We employed 8-plex isobaric Tags for Relative and Absolute Quantitation (iTRAQ), to profile the proteomes of two distinct panels of isogenic prostate cancer cells with varying growth and metastatic potentials, in order to identify novel biomarkers associated with progression. The LNCaP, LNCaP-Pro5, and LNCaP-LN3 panel of cells represent a model of androgen-responsive prostate cancer, while the PC-3, PC-3M, and PC-3M-LN4 panel represent a model of androgen-insensitive disease. RESULTS: Of the 245 unique proteins identified and quantified (>or=95% confidence; >or=2 peptides/protein), 17 showed significant differential expression (>or=+/-1.5), in at least one of the variant LNCaP cells relative to parental cells. Similarly, comparisons within the PC-3 panel identified 45 proteins to show significant differential expression in at least one of the variant PC-3 cells compared with parental cells. Differential expression of selected candidates was verified by Western blotting or immunocytochemistry, and corresponding mRNA expression was determined by quantitative real-time PCR (qRT-PCR). Immunostaining of prostate tissue microarrays for ERp5, one of the candidates identified, showed a significant higher immunoexpression in pre-malignant lesions compared with non-malignant epithelium (P < 0.0001, Mann-Whitney U-test), and in high Gleason grade (4-5) versus low grade (2-3) cancers (P < 0.05). CONCLUSIONS: Our study provides proof of principle for the application of an 8-plex iTRAQ approach to uncover clinically relevant candidate biomarkers for prostate cancer progression.

The key role of the western boundary in linking the AMOC strength to the north-south pressure gradient

A key idea in the study of the Atlantic meridional overturning circulation (AMOC) is that its strength is proportional to the meridional density gradient, or more precisely, to the strength of the meridional pressure gradient. A physical basis that would tell us how to estimate the relevant meridional pressure gradient locally from the density distribution in numerical ocean models to test such an idea, has been lacking however. Recently, studies of ocean energetics have suggested that the AMOC is driven by the release of available potential energy (APE) into kinetic energy (KE), and that such a conversion takes place primarily in the deep western boundary currents. In this paper, we develop an analytical description linking the western boundary current circulation below the interface separating the North Atlantic Deep Water (NADW) and Antarctic Intermediate Water (AAIW) to the shape of this interface. The simple analytical model also shows how available potential energy is converted into kinetic energy at each location, and that the strength of the transport within the western boundary current is proportional to the local meridional pressure gradient at low latitudes. The present results suggest, therefore, that the conversion rate of potential energy may provide the necessary physical basis for linking the strength of the AMOC to the meridional pressure gradient, and that this could be achieved by a detailed study of the APE to KE conversion in the western boundary current.

Vertical and horizontal processes in the global atmosphere and the maximum entropy production conjecture

The objective of this paper is to reconsider the Maximum Entropy Production conjecture (MEP) in the context of a very simple two-dimensional zonal-vertical climate model able to represent the total material entropy production due at the same time to both horizontal and vertical heat fluxes. MEP is applied first to a simple four-box model of climate which accounts for both horizontal and vertical material heat fluxes. It is shown that, under condition of fixed insolation, a MEP solution is found with reasonably realistic temperature and heat fluxes, thus generalising results from independent two-box horizontal or vertical models. It is also shown that the meridional and the vertical entropy production terms are independently involved in the maximisation and thus MEP can be applied to each subsystem with fixed boundary conditions. We then extend the four-box model by increasing its resolution, and compare it with GCM output. A MEP solution is found which is fairly realistic as far as the horizontal large scale organisation of the climate is concerned whereas the vertical structure looks to be unrealistic and presents seriously unstable features. This study suggest that the thermal meridional structure of the atmosphere is predicted fairly well by MEP once the insolation is given but the vertical structure of the atmosphere cannot be predicted satisfactorily by MEP unless constraints are imposed to represent the determination of longwave absorption by water vapour and clouds as a function of the state of the climate. Furthermore an order-of-magnitude estimate of contributions to the material entropy production due to horizontal and vertical processes within the climate system is provided by using two different methods. In both cases we found that approximately 40 mW m−2 K−1 of material entropy production is due to vertical heat transport and 5–7 mW m−2 K−1 to horizontal heat transport

Understanding and projecting sea level change

There is intense scientific and public interest in the Intergovernmental Panel on Climate Change (IPCC) projections of sea level for the twenty-first century and beyond. The Fourth Assessment Report (AR4) projections, obtained by applying standard methods to the results of the World Climate Research Programme Coupled Model Experiment, includes estimates of ocean thermal expansion, the melting of glaciers and ice caps (G&ICs), increased melting of the Greenland Ice Sheet, and increased precipitation over Greenland and Antarctica, partially offsetting other contributions. The AR4 recognized the potential for a rapid dynamic ice sheet response but robust methods for quantifying it were not available. Illustrative scenarios suggested additional sea level rise on the order of 10 to 20 cm or more, giving a wide range in the global averaged projections of about 20 to 80 cm by 2100. Currently, sea level is rising at a rate near the upper end of these projections. Since publication of the AR4 in 2007, biases in historical ocean temperature observations have been identified and significantly reduced, resulting in improved estimates of ocean thermal expansion. Models that include all climate forcings are in good agreement with these improved observations and indicate the importance of stratospheric aerosol loadings from volcanic eruptions. Estimates of the volumes of G&ICs and their contributions to sea level rise have improved. Results from recent (but possibly incomplete) efforts to develop improved ice sheet models should be available for the 2013 IPCC projections. Improved understanding of sea level rise is paving the way for using observations to constrain projections. Understanding of the regional variations in sea level change as a result of changes in ocean properties, wind-stress patterns, and heat and freshwater inputs into the ocean is improving. Recently, estimates of sea level changes resulting from changes in Earth's gravitational field and the solid Earth response to changes in surface loading have been included in regional projections. While potentially valuable, semi-empirical models have important limitations, and their projections should be treated with caution

Kinetic energy analysis of the response of the Atlantic meridional overturning circulation to CO2-forced climate change

Atmosphere–ocean general circulation models (AOGCMs) predict a weakening of the Atlantic meridional overturning circulation (AMOC) in response to anthropogenic forcing of climate, but there is a large model uncertainty in the magnitude of the predicted change. The weakening of the AMOC is generally understood to be the result of increased buoyancy input to the north Atlantic in a warmer climate, leading to reduced convection and deep water formation. Consistent with this idea, model analyses have shown empirical relationships between the AMOC and the meridional density gradient, but this link is not direct because the large-scale ocean circulation is essentially geostrophic, making currents and pressure gradients orthogonal. Analysis of the budget of kinetic energy (KE) instead of momentum has the advantage of excluding the dominant geostrophic balance. Diagnosis of the KE balance of the HadCM3 AOGCM and its low-resolution version FAMOUS shows that KE is supplied to the ocean by the wind and dissipated by viscous forces in the global mean of the steady-state control climate, and the circulation does work against the pressure-gradient force, mainly in the Southern Ocean. In the Atlantic Ocean, however, the pressure-gradient force does work on the circulation, especially in the high-latitude regions of deep water formation. During CO2-forced climate change, we demonstrate a very good temporal correlation between the AMOC strength and the rate of KE generation by the pressure-gradient force in 50–70°N of the Atlantic Ocean in each of nine contemporary AOGCMs, supporting a buoyancy-driven interpretation of AMOC changes. To account for this, we describe a conceptual model, which offers an explanation of why AOGCMs with stronger overturning in the control climate tend to have a larger weakening under CO2 increase

Revisiting the Earth's sea-level and energy budgets from 1961 to 2008

We review the sea-level and energy budgets together from 1961, using recent and updated estimates of all terms. From 1972 to 2008, the observed sea-level rise (1.8 ± 0.2 mm yr−1 from tide gauges alone and 2.1 ± 0.2 mm yr−1 from a combination of tide gauges and altimeter observations) agrees well with the sum of contributions (1.8 ± 0.4 mm yr−1) in magnitude and with both having similar increases in the rate of rise during the period. The largest contributions come from ocean thermal expansion (0.8 mm yr−1) and the melting of glaciers and ice caps (0.7 mm yr−1), with Greenland and Antarctica contributing about 0.4 mm yr−1. The cryospheric contributions increase through the period (particularly in the 1990s) but the thermosteric contribution increases less rapidly. We include an improved estimate of aquifer depletion (0.3 mm yr−1), partially offsetting the retention of water in dams and giving a total terrestrial storage contribution of −0.1 mm yr−1. Ocean warming (90% of the total of the Earth's energy increase) continues through to the end of the record, in agreement with continued greenhouse gas forcing. The aerosol forcing, inferred as a residual in the atmospheric energy balance, is estimated as −0.8 ± 0.4 W m−2 for the 1980s and early 1990s. It increases in the late 1990s, as is required for consistency with little surface warming over the last decade. This increase is likely at least partially related to substantial increases in aerosol emissions from developing nations and moderate volcanic activity

Features for detection of Parkinson's disease tremor from local field potentials of the subthalamic nucleus

Deep Brain Stimulation (DBS) is a treatment routinely used to alleviate the symptoms of Parkinson's disease (PD). In this type of treatment, electrical pulses are applied through electrodes implanted into the basal ganglia of the patient. As the symptoms are not permanent in most patients, it is desirable to develop an on-demand stimulator, applying pulses only when onset of the symptoms is detected. This study evaluates a feature set created for the detection of tremor - a cardinal symptom of PD. The designed feature set was based on standard signal features and researched properties of the electrical signals recorded from subthalamic nucleus (STN) within the basal ganglia, which together included temporal, spectral, statistical, autocorrelation and fractal properties. The most characterized tremor related features were selected using statistical testing and backward algorithms then used for classification on unseen patient signals. The spectral features were among the most efficient at detecting tremor, notably spectral bands 3.5-5.5 Hz and 0-1 Hz proved to be highly significant. The classification results for determination of tremor achieved 94% sensitivity with specificity equaling one.

The impact of a seasonally ice free Arctic Ocean on the temperature, precipitation and surface mass balance of Svalbard

The observed decline in summer sea ice extent since the 1970s is predicted to continue until the Arctic Ocean is seasonally ice free during the 21st Century. This will lead to a much perturbed Arctic climate with large changes in ocean surface energy flux. Svalbard, located on the present day sea ice edge, contains many low lying ice caps and glaciers and is expected to experience rapid warming over the 21st Century. The total sea level rise if all the land ice on Svalbard were to melt completely is 0.02 m. The purpose of this study is to quantify the impact of climate change on Svalbard’s surface mass balance (SMB) and to determine, in particular, what proportion of the projected changes in precipitation and SMB are a result of changes to the Arctic sea ice cover. To investigate this a regional climate model was forced with monthly mean climatologies of sea surface temperature (SST) and sea ice concentration for the periods 1961–1990 and 2061–2090 under two emission scenarios. In a novel forcing experiment, 20th Century SSTs and 21st Century sea ice were used to force one simulation to investigate the role of sea ice forcing. This experiment results in a 3.5 m water equivalent increase in Svalbard’s SMB compared to the present day. This is because over 50 % of the projected increase in winter precipitation over Svalbard under the A1B emissions scenario is due to an increase in lower atmosphere moisture content associated with evaporation from the ice free ocean. These results indicate that increases in precipitation due to sea ice decline may act to moderate mass loss from Svalbard’s glaciers due to future Arctic warming.

Protein structure prediction servers at University College London

A number of state-of-the-art protein structure prediction servers have been developed by researchers working in the Bioinformatics Unit at University College London. The popular PSIPRED server allows users to perform secondary structure prediction, transmembrane topology prediction and protein fold recognition. More recent servers include DISOPRED for the prediction of protein dynamic disorder and DomPred for domain boundary prediction.

Predicting metal-binding site residues in low-resolution structural models

The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site.

Precise calculations of the existence of multiple AMOC equilibria in coupled climate models Part I: equilibrium states

This study examines criteria for the existence of two stable states of the Atlantic Meridional Overturning Circulation (AMOC) using a combination of theory and simulations from a numerical coupled atmosphere–ocean climate model. By formulating a simple collection of state parameters and their relationships, the authors reconstruct the North Atlantic Deep Water (NADW) OFF state behavior under a varying external salt-flux forcing. This part (Part I) of the paper examines the steady-state solution, which gives insight into the mechanisms that sustain the NADW OFF state in this coupled model; Part II deals with the transient behavior predicted by the evolution equation. The nonlinear behavior of the Antarctic Intermediate Water (AAIW) reverse cell is critical to the OFF state. Higher Atlantic salinity leads both to a reduced AAIW reverse cell and to a greater vertical salinity gradient in the South Atlantic. The former tends to reduce Atlantic salt export to the Southern Ocean, while the latter tends to increases it. These competing effects produce a nonlinear response of Atlantic salinity and salt export to salt forcing, and the existence of maxima in these quantities. Thus the authors obtain a natural and accurate analytical saddle-node condition for the maximal surface salt flux for which a NADW OFF state exists. By contrast, the bistability indicator proposed by De Vries and Weber does not generally work in this model. It is applicable only when the effect of the AAIW reverse cell on the Atlantic salt budget is weak.

Non-D9-tetrahydrocannabinol phytocannabinoids stimulate feeding in rats

Cannabinoid type 1 receptor-mediated appetite stimulation by D9tetrahydrocannabinol (D9THC) is well understood. Recently, it has become apparent that non-D9THC phytocannabinoids could also alter feeding patterns. Here, we show definitively that non-D9THC phytocannabinoids stimulate feeding. Twelve male, Lister-Hooded rats were prefed to satiety prior to administration of a standardized cannabis extract or to either of two mixtures of pure phytocannabinoids (extract analogues) comprising the phytocannabinoids present in the same proportions as the standardized extract (one with and one without D9THC). Hourly intake and meal pattern data were recorded and analysed using two-way analysis of variance followed by one-way analysis of variance and Bonferroni post-hoc tests. Administration of both extract analogues significantly increased feeding behaviours over the period of the test. All three agents increased hour-one intake and meal-one size and decreased the latency to feed, although the zero-D9THC extract analogue did so to a lesser degree than the high-D9THC analogue. Furthermore, only the analogue containing D9THC significantly increased meal duration. The data confirm that at least one non-D9THC phytocannabinoid induces feeding pattern changes in rats, although further trials using individual phytocannabinoids are required to fully understand the observed effects.