Marine proteomics: generation of sequence tags for dissolved proteins in seawater using tandem mass spectrometry

Dissolved proteins in seawater samples from the Gulf of Mexico were concentrated using tangential flow ultrafiltration and methanol/chloroform/water precipitation. Following concentration and purification, two different separation methods were employed. In one method, intact proteins were separated by SDS–PAGE and digested enzymatically in-gel. In the second method, the peptides resulting from a solution proteolytic digest of the whole protein pellet mixture were separated by capillary HPLC. In both methods, the final chromatographic separation was coupled on-line with a mass spectrometer using an electrospray interface, and peptide CID spectra were collected using tandem mass spectrometry (MS). De novo sequencing of the peptide tandem mass spectra generated short amino acid sequences (peptide tags) that were used to search databases for protein class and source information. Trends of conserved sequences for two specific classes of proteins were observed: membrane/envelope proteins and enzymes. Similarity searching of peptide tags produced identification of conserved sequences from several protein homologues originating from many different species, including: long chain fatty acyl CoA synthetase, anthranilate synthase, ribulose bisphosphate carboxylase, and luminal binding protein. These results provide new insight into the sources and production mechanisms for dissolved organic matter (DOM), as there is direct evidence for dissolved proteins other than the bacterial outer membrane proteins reported by Tanoue et al. Furthermore, the data presented herein support the idea that physical protection and selective preservation are not mutually exclusive survival mechanisms, but rather these two models are dependent upon one another for explaining the survival of refractory dissolved proteins in seawater.     

Evaluation of NASA GISS Post-CMIP5 Single Column Model Simulated Clouds and Precipitation Using ARM Southern Great Plains Observations

The planetary boundary layer turbulence and moist convection parameterizations have been modified recently in the NASA Goddard Institute for Space Studies(GISS) Model E2 atmospheric general circulation model(GCM; post-CMIP5,hereafter P5). In this study, single column model(SCM P5) simulated cloud fractions(CFs), cloud liquid water paths(LWPs)and precipitation were compared with Atmospheric Radiation Measurement(ARM) Southern Great Plains(SGP) groundbased observations made during the period 2002–08. CMIP5 SCM simulations and GCM outputs over the ARM SGP region were also used in the comparison to identify whether the causes of cloud and precipitation biases resulted from either the physical parameterization or the dynamic scheme. The comparison showed that the CMIP5 SCM has difficulties in simulating the vertical structure and seasonal variation of low-level clouds. The new scheme implemented in the turbulence parameterization led to significantly improved cloud simulations in P5. It was found that the SCM is sensitive to the relaxation time scale. When the relaxation time increased from 3 to 24 h, SCM P5-simulated CFs and LWPs showed a moderate increase(10%–20%) but precipitation increased significantly(56%), which agreed better with observations despite the less accurate atmospheric state. Annual averages among the GCM and SCM simulations were almost the same, but their respective seasonal variations were out of phase. This suggests that the same physical cloud parameterization can generate similar statistical results over a long time period, but different dynamics drive the differences in seasonal variations. This study can potentially provide guidance for the further development of the GISS model.     

Machine Learning Can Assign Geologic Basin to Produced Water Samples Using Major Ion Geochemistry

Natural Resources Research - Understanding the geochemistry of waters produced during petroleum extraction is essential to informing the best treatment and reuse options, which can potentially be...     

Tectonic configuration of the Apuseni–Banat—Timok–Srednogorie belt, Balkans-South Carpathians, constrained by high precision Re–Os molybdenite ages

The Apuseni–Banat–Timok–Srednogorie magmatic–metallogenic belt (ABTS belt), forms a substantial metallogenic province in the Balkan-South Carpathian system in southeastern Europe. The belt hosts porphyry, skarn, and epithermal deposits mined since pre-Roman times. Generally, the deposits, prospects, and occurrences within the belt are linked to magmatic centers of calc-alkaline affinity. Fifty-one rhenium-osmium (Re–Os) ages and Re concentration data for molybdenites define systematic geochronologic trends and constrain the geochemical-metallogenic evolution of the belt in space and time. From these data and additional existing geologic-geochemical data, a general tectonic history for the belt is proposed. Mineralization ages in Apuseni-Banat, Timok, and Panagyurishte (the central district of the larger E–W Srednogorie Zone) range from 72–83, 81–88, and 87–92 Ma, respectively, and clearly document increasing age from the northwestern districts to the southeastern districts. Further, Re–Os ages suggest rapidly migrating pulses of Late Cretaceous magmatic–hydrothermal activity with construction of deposits in ~1 m.y., districts in ~10 m.y., and the entire 1,500 km belt in ~20 m.y. Ages in both Timok and Panagyurishte show systematic younging, while deposit ages in Banat and Apuseni are less systematic reflecting a restricted evolution of the tectonic system. Systematic differences are also observed for molybdenite Re concentrations on the belt scale. Re concentrations generally range from hundreds to thousands of parts per million, typical of subduction-related Cu–Au–Mo–(PGE) porphyry systems associated with the generation of juvenile crust. The geochronologic and geochemical trends are compatible with proposed steepening of subducting oceanic slab and relaxation of upper continental plate compression. Resulting influx of sub-continental mantle lithosphere (SCML) and asthenosphere provide a fertile metal source and heat, while the subducting slab contributes connate and mineral dehydration fluids, which facilitate partial melting and metal leaching of SCML and asthenosphere. Cu–Au–Mo–(PGE) porphyry deposits may develop where melts are trapped at shallow crustal levels, often with associated volcanism and epithermal-style deposits (South Banat, Timok, and Panagyurishte). Mo–Fe–Pb–Zn skarn deposits may develop where felsic melts are trapped adjacent to Mesozoic limestones at moderate crustal levels (North Banat and Apuseni). Systematic spatial variations in deposit style, commodity enrichment, Re–Os ages, and Re concentrations support specific tectonic processes that led to ore formation. In a post-collisional setting, subduction of Vardar oceanic crust may have stalled, causing slab steepening and rollback. The slab rollback relaxes compression, facilitating and enhancing orogenic collapse of previously thickened Balkan-South Carpathian crust. The progression of coupled rollback-orogenic collapse is evidenced by the width of Late Cretaceous extensional basins and northward younging of Re–Os ages, from Panagyurishte (~60 km; 92–87 Ma) to Timok (~20 km; 88–81 Ma) to Apuseni-Banat (~5 km; 83–72 Ma). Generation of a well-endowed mineral belt, such as the ABTS, requires a temporally and spatially restricted window of magmatic–hydrothermal activity. This window is quickly opened as upper plate compression relaxes, thereby inducing melt generation and ingress of melt to higher crustal levels. The window is just as quickly closed as upper plate compression is reinstated. The transient tectonic state responsible for economic mineralization in the ABTS belt may be a paleo-analogue to transient intervals in the present subduction tectonics of SE Asia where much mineral wealth has been created in the last few million years.     

Virtual observatories for space and solar physics research

As soon as the first data became available online over the Internet, it was obvious that different sites holding related datasets should appear to the end user as a single data system, even if the data itself is stored at multiple locations. To achieve this objective in the context of continuing parallel development of multiple data centres, in 2003 several actors in the realm of space plasmas created the international consortium Space Physics Archive Search and Extract (SPASE). Since 2005 US participation in SPASE has been supported by NASA, and early in 2006 NASA funded five new Virtual Observatories to cater for different aspects of solar system plasma science. This paper outlines the current status of the SPASE effort, the opportunities it offers, its specificities with respect to other parts of the astronomical virtual observatory, and the possibilities it offers for space weather.

The filtering capacity of a tropical riverine wetland: II. Sediment and nutrient balances

The ability of wetlands to improve the quality of water has long been recognized and has led to the proliferation of wetlands as a means to treat diffuse and point source pollutants from a range of land uses. However, much of the existing research has been undertaken in temperate climates with a paucity of information on the effectiveness of wetlands, particularly natural wetlands, in tropical regions. This paper contributes to addressing this issue by presenting a comprehensive measurement based assessment of the potential for a naturally occurring tropical riverine wetland to improve the quality of the water entering it. We found small net imports and exports of sediment to/from the wetland in individual years, but over the longer term this kind of wetland is neither a sink nor source of sediment. In contrast, phosphorus was continually removed by the wetland with an overall net reduction of 14%. However, it should be noted that there is no ‘permanent’ gaseous loss mechanism for phosphorus, and its removal from the water column is equal to its accumulation in the wetland soil. We found very little removal of nitrogen by this type of wetland from several analyses including: (i) Surface and groundwater fluxes, (ii) Estimation of water column and soil denitrification rates, (iii) Wetland residence times, and (iv) Hydraulic loading. We also found no clear evidence for transformation of nitrogen to more or less bio‐available forms. Hence, while the benefits of using wetlands to improve water quality in controlled environments have been demonstrated in the literature, these benefits may not always be directly translated to unmanaged natural wetland systems when there is strong seasonality in flows and short residence time during the periods of maximum sediment and nutrient load. Copyright © 2011 John Wiley & Sons, Ltd.     

Isotopic Ratios Reveal Mixed Seasonal Variation Among Fishes from Two Subtropical Estuarine Systems

Characterizing dietary resources and species interactions in estuaries is challenging, particularly when considering the dynamic nature of these ecosystems, the ranges in body sizes of species, and the potential for trophic roles to vary with ontogeny. We examined the influence of season and location on relationships between body size and δ¹⁵N, δ¹³C, and δ³⁴S values across a range of fishes from two subtropical estuaries. The results suggest that isotopic values of estuarine fishes are independent of body size. However, seasonal variation propagated throughout the assemblage as the majority of fishes integrated different δ¹⁵N, δ¹³C, or δ³⁴S values. The absence of δ¹⁵N–, δ¹³C–, and δ³⁴S–body size relationships suggests that either (1) dietary preference of these fishes do not shift within the range of body sizes sampled, (2) these fishes shift to an alternate diet that is not isotopically distinct, or (3) that spatial and temporal variation in isotopic signatures of prey negate any size-based relationships. Seasonal variability in the isotopic values of these fishes suggests either movement to an alternative habitat or a shift in organic matter source associated with the transition of dry to wet seasons. Moreover, variance distributions of the best-fit models indicate that seasonal dietary preferences of conspecifics do not vary over moderate spatial scales. Seasonal variability among fishes in these estuaries suggests plasticity in feeding strategies that may afford greater adaptive flexibility to these species in response to changes in food availability resulting from variable environmental conditions.     

Modeling IR spectral energy distributions: a?pilot study of?starburst parameters and silicate absorption curves for some GOALS galaxies

This paper describes a pilot study into the spectral energy distribution (SED) fitting and the derivation of physical parameters for 19 galaxies observed as part of the Great Observatories All-sky LIRG Survey (GOALS) survey as observed with the Spitzer Space Telescope. For this we have used the pan-spectral fitting tools developed in a series of papers by Dopita and his co-workers. We show that the standard Lee and Draine ??astronomical silicate?? model cannot provide a good fit to the silicate absorption features as observed in the heavily dust-extinguished (A _V??50 mag.) starbursts. We have derived an empirical fit to the ??starburst silicate?? absorption in these objects. This absorption curve is consistent with the silicate grains being systematically larger in starburst environments than in the local Galactic interstellar medium. We demonstrate the sensitivity of the SED fitting to each of the fitted parameters, and derive these parameters for those galaxies which do not have an embedded AGN. This technique is simple and provides reasonably robust and uniform parameters for the starburst, especially as far as the star formation rate, population of old stars, compactness of the starburst region and total foreground extinction are concerned. However, the chemical abundances and the optical extinction cannot be reliably determined by this analysis, and optical SEDs will also be required to provide a complete characterization of the starburst region and of the surrounding galaxy.