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.     

Exploring the Effectiveness of Outreach Strategies in Conservation Projects: The Case of the Audubon Toyota TogetherGreen Program

Successfully engaging target audiences represents a key challenge for environmental conservation projects. In this study, we examined 354 conservation projects implemented across the United States with the intention of systematically exploring the relationships between different forms of outreach (in particular, message content and delivery) and self-reported project outcomes. Using end-of-program retrospective surveys, we found that experiential engagement and directly demonstrating and/or communicating the ease of potential conservation actions were most consistently related to achieving desired project outcomes. Although it was thought to be largely effective by project managers, we found that focusing on equipping audiences with new knowledge was negatively related to conservation outcomes. Measured outreach variables explained between 15% and 17% of the variance in project outcomes, suggesting a wide variety of unmeasured factors at play. We discuss insights relevant to engaging target audiences in future U.S. conservation projects.     

Yesterday's Freeway Network of Tomorrow

In 1939, the Futurama exhibit at the New York World's Fair amazed visitors with its diorama showing futuristic freeways crossing the countryside and reshaping cities. After the fair, the exhibit's designer, Norman Bel Geddes, elaborated the model into a proposal for a national freeway network. This paper examines the network structure and geographic dimensions of Bel Geddes's vision and compares it to the Interstate Highway System, created several years later. Despite the futuristic trappings inherited from the Futurama model, the two networks are surprisingly similar except in their relation to cities, which Bel Geddes's network avoids. The majority of elements in Bel Geddes's system have been incorporated into actual routes and networks, and it can be expected that his system would have gone through many of the same adaptations to changing economic, environmental, and political circumstances as the Interstate Highway System.     

Ti-in-zircon thermometry applied to contrasting Archean metamorphic and igneous systems

Ti-in-zircon thermometry with SHRIMP II multi-collector has been applied to two well-documented Archean igneous and metamorphic samples from southern West Greenland. Zircons from 2.71 Ga partial melt segregation G03/38 formed in a small (< 1 m³), closed system within a mafic rock under high pressure granulite facies conditions. Results of 14 Ti analyses present a mean apparent zircon crystallization temperature of 679 ± 11 °C, underestimating independent garnet-clinopyroxene thermometry by 20–50 °C but consistent with reduced a_TiO2 in this system. 36 spot analysis on 15 zircons from 3.81 Ga meta-tonalite G97/18, with an estimated magmatic temperature > 1000 °C, yield a low-temperature focused normal distribution with a mean of 683 ± 32 °C, further demonstrated by high resolution Ti mapping of two individual grains. This distribution is interpreted to represent the temperature of the residual magma at zircon saturation, late in the crystallization history of the tonalite. Hypothetically, Ti-in-zircon thermometry on Eoarchaean detrital zircons sourced from such a high temperature tonalite would present a low-temperature biased image of the host magma, which could be misconstrued as being a minimum melt granite. Multiple analyses from individual zircons can yield complex Ti distributions and associated apparent temperature patterns, reflecting cooling history and local chemical environments in large magma chambers. In addition to inclusions and crystal imperfections, which can yield apparent high temperature anomalies, zircon surfaces can also record extreme (> 1000 °C) apparent Ti temperatures. In our studies these were traced to ⁴⁹Ti (or a molecular isobaric interference) contamination derived from the double sided adhesive tape used in sample preparation, and should not be assigned geological significance.     

Natural Disturbance Shapes Benthic Intertidal Macroinvertebrate Communities of High Latitude River Deltas

Unlike lower latitude coastlines, the estuarine nearshore zones of the Alaskan Beaufort Sea are icebound and frozen up to 9 months annually. This annual freezing event represents a dramatic physical disturbance to fauna living within intertidal sediments. The main objectives of this study were to describe the benthic communities of Beaufort Sea deltas, including temporal changes and trophic structure. Understanding benthic invertebrate communities provided a baseline for concurrent research on shorebird foraging ecology at these sites. We found that despite continuous year-to-year episodes of annual freezing, these estuarine deltas are populated by a range of invertebrates that represent both marine and freshwater assemblages. Freshwater organisms like Diptera and Oligochaeta not only survive this extreme event, but a marine invasion of infaunal organisms such as Amphipoda and Polychaeta rapidly recolonizes the delta mudflats following ice ablation. These delta sediments of sand, silt, and clay are fine in structure compared to sediments of other Beaufort Sea coastal intertidal habitats. The relatively depauperate invertebrate community that ultimately develops is composed of marine and freshwater benthic invertebrates. The composition of the infauna also reflects two strategies that make life on Beaufort Sea deltas possible: a migration of marine organisms from deeper lagoons to the intertidal and freshwater biota that survive the 9-month ice-covered period in frozen sediments. Stable isotopic analyses reveal that both infaunal assemblages assimilate marine and terrestrial sources of organic carbon. These results provide some of the first quantitative information on the infaunal food resources of shallow arctic estuarine systems and the long-term persistence of these invertebrate assemblages. Our data help explain the presence of large numbers of shorebirds in these habitats during the brief summer open-water period and their trophic importance to migrating waterfowl and nearshore populations of estuarine fishes that are the basis of subsistence lifestyles by native inhabitants of the Beaufort Sea coast.     

The stratigraphic and geographic distribution of giant craters and remobilised sediment mounds on the mid Norway margin,and their relation to long term fluid flow

Large craters associated with mounds of remobilised sediment have been recently mapped on the mid Norway margin in the Møre Basin. These craters and mounds may be linked to the long term migration of fluids upwards from the lower levels of the Møre Basin which exploit hydrothermal vent complexes emplaced in the late Paleocene and early Eocene. All of the craters are located on a regionally correlative seismic surface that is correlated with the basal shear plane of Slide W, a slide located at the base of the Plio-Pleistocene Naust Formation. The Craters are positioned in the western area of the Møre Basin at the foot of the continental slope on the crests and flanks of Miocene domes, where Oligocene biosiliceous ooze subcrops on the basal shear surface of Slide W. Not all of the craters are filled by Slide W. Mounds are emplaced above those craters which are filled by Slide W on the top surface of Slide W. Stratal relationships show that the mounds were emplaced on the paleo-seabed. We present and discuss two models that illustrate processes that may have been involved in the formation of craters and remobilisation of sediments. In one model, an eruption of fluid from beneath remobilises ooze into ooze mounds in a single event triggering slope failure, whereas in the other model the emplacement of Slide W and later slides loads low density ooze causing it to undergo liquefaction, a process which may have been facilitated by the trapping of continuous long term fluid migrating from beneath, causing the ooze to remobilise into ooze mounds in two or more events.     

Intermediate granulite produced by transformation of eclogite at a felsic granulite contact,in Blanský les,Bohemian Massif

Layers or bodies of intermediate granulite on scales from a centimetre to a hundred metres occur commonly within the felsic granulite massifs of the Bohemian Massif. Their origin is enigmatic in that they commonly have complex microstructures that are difficult to interpret, and therefore even the sequence of crystallization of minerals is uncertain. At Kle?, in the Blanský les massif, there is a revealing outcrop in a low‐strain zone in which it is clear that intermediate granulite can form by the interaction of felsic granulite with eclogite. The eclogite, retains garnet from its eclogite heritage, the grains at least partially isolated from the matrix by a plagioclase corona. The original omphacite‐dominated matrix of the eclogite now consists of recrystallized diopsidic clinopyroxene, orthopyroxene and plagioclase, with minor brown amphibole and quartz. The modification of the eclogite is dominated by the addition of just K₂O and H₂O, rather than all the elements that would be involved if the process was one of pervasive melt infiltrations. This suggests that the main process involved is diffusion, with the source being the felsic granulite, or local partial melt of the granulite. The diffusion occurred at ~950 °C and 12 kbar, with the main observed effects being (i) the un‐isolation and preferential destruction of the interior part of some of the garnet grains by large idiomorphic ternary feldspar; (ii) textural modification of the matrix primarily involving the recrystallization of clinopyroxene into large poikiloblasts containing inclusions of ternary plagioclase; and (iii) conversion of low‐K plagioclase in the matrix into ternary feldspar by incorporation of the diffused‐in K₂O. The phase equilibria in the intermediate granulite are consistent with the chemical potential relationships that would be superimposed on the original eclogite by the felsic granulite at 950 °C and 12 kbar.     

Does canopy wetness matter? Evapotranspiration from a subtropical montane cloud forest in Taiwan

Evapotranspiration (ET) and canopy wetness were measured over a 2‐year intensive field campaign at the Chi‐Lan Mountain cloud forest site in Taiwan. Eddy covariance and sap flow methods were applied to measure ET and tree sap flow of the endemic yellow cypress (Chamaecyparis obtusa var. formosana). ET was 553 mm yr^?1 over the study period with an annual rainfall and fog deposition of 4893 and 288 mm yr^–1, respectively. The duration of canopy wetness exceeded actual fog or rain events (mostly in the afternoon), and the intercepted water was evaporated later in the following dry morning. The cumulative wet duration accounted for 52% of time over the study period, which was longer than the duration of rainfall and fog altogether (41%). As it adapted to the extremely moist environment, the yellow cypress behaved in a wet‐enhanced/dry‐reduced water use strategy and was sensitive to short periods of dry atmosphere with high evaporation potential. During dry days, the sap flow rate rose quickly after dawn and led to conservative water use through midday and the afternoon. During periodically wet days, the canopy was mostly wetted in the morning, and the interception evaporation contributed largely to the morning ET. The initiation of morning sap flow was postponed 1–3 h, and the sap flow rate tended to peak later at midday. The midday canopy conductance was higher in the periodically wet days (10.6 mm s^–1) as compared with 7.6 mm s^?1 in the dry days. Consequently, the dry‐reduced water use strategy led to much lower annual ET with respect to the available energy (~46%) and high precipitation input (~11%). The moist‐adapted ecohydrology we report reveals the vulnerability of montane cloud forests to prolonged fog‐free periods. More research is urgently needed to better understand the resilience of these ecosystems and formulate adaptive management plans. Copyright © 2012 John Wiley & Sons, Ltd.     

Refining the image of the San Andreas Fault near Parkfield, California using a finite difference travel time computation technique

The Parkfield Area Seismic Observatory (PASO) was a dense, telemetered seismic array that operated for nearly 2 years in a 15 km aperture centered on the San Andreas Fault Observatory at Depth (SAFOD) drill site. The main objective of this deployment was to refine the locations of earthquakes that will serve as potential targets for SAFOD drilling and in the process develop a high (for passive seismological techniques) resolution image of the fault zone structure. A challenging aspect of the analysis of this data set was the known existence of large (20–25%) contrasts in seismic wavespeed across the San Andreas Fault. The resultant distortion of raypaths could challenge the applicability of approximate ray tracing techniques. In order to test the sensitivity of our hypocenter locations and tomographic image to the particular ray tracing and inversion technique employed, we compare an initial determination of locations and structure developed using a coarse grid and an approximate ray tracer [Thurber, C., Roecker, S., Roberts, K., Gold, M., Powell, M.L. , and Rittger, K., 2003. Earthquake locations and three-dimensional fault zone structure along the creeping section of the San Andreas fault near Parkfield, CA: Preparing for SAFOD, Geophys. Res. Lett., 30 3, 10.1029/2002GL016004.] with one derived from a relatively fine grid and an application of a finite difference algorithm [Hole, J.A., and Zelt, B.C., 1995. 3-D finite-difference reflection traveltimes, Geophys. J. Int., 121, 2, 427–434.]. In both cases, we inverted arrival-time data from about 686 local earthquakes and 23 shots simultaneously for earthquake locations and three-dimensional Vp and Vp/Vs structure. Included are data from an active source seismic experiment around the SAFOD site as well as from a vertical array of geophones installed in the 2-km-deep SAFOD pilot hole, drilled in summer 2002. Our results show that the main features of the original analysis are robust: hypocenters are located beneath the trace of the fault in the vicinity of the drill site and the positions of major contrasts in wavespeed are largely the same. At the same time, we determine that shear wave speeds in the upper 2 km of the fault zone are significantly lower than previously estimated, and our estimate of the depth of the main part of the seismogenic zone decreases in places by  100 m. Tests using “virtual earthquakes” (borehole receiver gathers of picks for surface shots) indicate that our event locations near the borehole currently are accurate to about a few tens of meters horizontally and vertically.