CiteULike: mblwhoi's library [1105 articles]

Massive Horizontal Gene Transfer in Bdelloid Rotifers

Eugene Gladyshev — 2008-06-03T19:30:19-00:00

Science, Vol. 320, No. 5880. (30 May 2008), pp. 1210-1213.

Horizontal gene transfer in metazoans has been documented in only a few species and is usually associated with endosymbiosis or parasitism. By contrast, in bdelloid rotifers we found many genes that appear to have originated in bacteria, fungi, and plants, concentrated in telomeric regions along with diverse mobile genetic elements. Bdelloid proximal gene-rich regions, however, appeared to lack foreign genes, thereby resembling those of model metazoan organisms. Some of the foreign genes were defective, whereas others were intact and transcribed; some of the latter contained functional spliceosomal introns. One such gene, apparently of bacterial origin, was overexpressed in Escherichia coli and yielded an active enzyme. The capture and functional assimilation of exogenous genes may represent an important force in bdelloid evolution. 10.1126/science.1156407

Nansen-bottle stations at the Woods Hole Oceanographic Institution

Bruce Warren — 2008-06-11T18:30:31-00:00

Deep Sea Research Part I: Oceanographic Research Papers, Vol. 55, No. 4. (April 2008), pp. 379-395.

Nansen-bottle stations were occupied by ships and personnel of the Woods Hole Oceanographic Institution from 1931 to about 1981. Most of these data are in archives, but using them intelligently to depict the state of the ocean and to assess time changes in it requires knowing how the observations were made, what accuracies can be assigned to them, and generally how to approach them. This report describes the evolving methods on Woods Hole stations for measuring temperature, depth of observation, salinity, and dissolved-oxygen concentration, and for determining station position. Accuracies generally improved over time, although estimates from the early years are sparse, and even later there is indefiniteness. Analytical error is to be distinguished from sloppy sample collection and other blunders. The routine for carrying out Nansen-bottle stations, from the late 1950s through the 1970s, is reviewed.

Bipolar, anastral spindle development in artificially activated sea urchin eggs

John Henson — 2008-06-11T18:27:54-00:00

Developmental Dynamics, Vol. 237, No. 5. (2008), pp. 1348-1358.

The mitotic apparatus of the early sea urchin embryo is the archetype example of a centrosome-dominated, large aster spindle organized by means of the centriole of the fertilizing sperm. In this study, we tested the hypothesis that artificially activated sea urchin eggs possess the capacity to assemble the anastral, bipolar spindles present in many acentrosomal systems. Control fertilized Lytechinus pictus embryos and ammonia-activated eggs were immunolabeled for tubulin, centrosomal material, the spindle pole structuring protein NuMA and the mitotic kinesins MKLP1/Kinesin-6, Eg5/Kinesin-5, and KinI/Kinesin-13. Confocal imaging showed that a subset of ammonia-activated eggs contained bipolar mini-spindles that were anastral; displayed metaphase and anaphase-like stages; labeled for centrosomal material, NuMA, and the three mitotic kinesins; and were observed in living eggs using polarization optics. These results suggest that spindle structural and motor proteins have the ability to organize bipolar, anastral spindles in sea urchin eggs activated in the absence of the paternal centriole.

Lead Sequestration and Species Redistribution During Soil Organic Matter Decomposition

Andrew Schroth — 2008-06-11T18:21:06-00:00

Environ. Sci. Technol., Vol. 42, No. 10. (15 May 2008), pp. 3627-3633.

Abstract: The turnover of soil organic matter (SOM) maintains a dynamic chemical environment in the forest floor that can impact metal speciation on relatively short timescales. Here we measure the speciation of Pb in controlled and natural organic (O) soil horizons to quantify changes in metal partitioning during SOM decomposition in different forest litters. We provide a link between the sequestration of pollutant Pb in O-horizons, estimated by forest floor Pb inventories, and speciation using synchrotron-based X-ray fluorescence and X-ray absorption spectroscopy. When Pb was introduced to fresh forest Oi samples, it adsorbed primarily to SOM surfaces, but as decomposition progressed over two years in controlled experiments, up to 60% of the Pb was redistributed to pedogenic birnessite and ferrihydrite surfaces. In addition, a significant fraction of pollutant Pb in natural soil profiles was associated with similar mineral phases (~2035%) and SOM (~6580%). Conifer forests have at least 2-fold higher Pb burdens in the forest floor relative to deciduous forests due to more efficient atmospheric scavenging and slower organic matter turnover. We demonstrate that pedogenic minerals play an important role in surface soil Pb sequestration, particularly in deciduous forests, and should be considered in any assessment of pollutant Pb mobility.

Identification of larval sea basses (Centropristis spp.) using ribosomal DNA-specific molecular assays

Mark Vandersea — 2008-06-11T18:19:57-00:00

Fishery Bulletin, Vol. 106, No. 2. (2008), pp. 183-193.

The identification of sea bass (Centropristis) larvae to species is difficult because of similar morphological characters, spawning times, and overlapping species ranges. Black sea bass (Centropristis striata) is an important fishery species and is currently considered to be overfished south of Cape Hatteras, North Carolina. We describe methods for identifying three species of sea bass larvae using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) assays based on species-specific amplification of rDNA internal transcribed spacer reg ions. The assays were tested against DNA of ten other cooccurring reef fish species to ensure the assay’s specificity. Centropristis larvae were collected on three cruises during cross-shelf transects and were used to validate the assays. Seventysix Centropristis larvae were assayed and 69 (91%) were identified successfully. DNA was not amplified from 5% of the larvae and identification was inconclusive for 3% of the larvae. These assays can be used to identify sea bass eggs and larvae and will help to assess spawning locations, spawning times, and larval dispersal.

Mineralization of ancient carbon in the subsurface of riparian forests

Noel Gurwick — 2008-05-12T14:29:54-00:00

Journal of Geophysical Research, Vol. 113 (10 May 2008), G02021.

Microbial activity in saturated, subsurface sediments in riparian forests may be supported by recent photosynthate or ancient (>500 ybp) soil organic carbon (SOC) in buried horizons. Metabolism of ancient SOC may be particularly important in riparian zones, considered denitrification hot spots, because denitrification in the riparian subsurface is often C-limited, because buried horizons intersect deep flow paths, and because low C mineralization rates can support ecosystem-relevant rates of denitrification. Buried horizons are common where alluvial processes (stream migration, overbank flow) have dominated riparian evolution. Our objectives were to determine: (1) the extent to which ancient SOC directly supports subsurface microbial activity; (2) whether different C sources support microbial activity in alluvial versus glaciofluvial riparian zones; and (3) how microbial use of ancient SOC varies with depth. In situ groundwater incubations and 14C dating of dissolved inorganic carbon revealed that ancient SOC mineralization was common, and that it constituted 31–100% of C mineralization 2.6 m deep at one site, at rates sufficient to influence landscape N budgets. Our data failed to reveal consistent spatial patterns of microbially available ancient C. Although mineralized C age increased with depth at one alluvial site, we observed ancient C metabolism 150 cm deep at a glaciofluvial site, suggesting that subsurface microbial activity in riparian zones does not vary systematically between alluvial and glaciofluvial hydrogeologic settings. These findings underscore the relevance of ancient C to contemporary ecosystem processes and the challenge of using mappable surface features to identify subsurface ecosystem characteristics or riparian zone N-sink strength.

Color matching on natural substrates in cuttlefish, Sepia officinalis

Lydia Mäthger — 2008-06-11T18:14:59-00:00

Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology, Vol. 194, No. 6. (14 June 2008), pp. 577-585.

Abstract The camouflaging abilities of cuttlefish (Sepia officinalis) are remarkable and well known. It is commonly believed that cuttlefish—although color blind—actively match various colors of their immediate surroundings, yet no quantitative data support this notion. We assembled several natural substrates chosen to evoke the three basic types of camouflaged body patterns that cuttlefish express (uniform/stipple, mottle, and disruptive) and measured the spectral reflectance of the camouflaged pattern and the respective background using a fiber optic spectrometer. We demonstrate that the reflectance spectra of cuttlefish skin patterns correlate closely with the spectra of these natural substrates. Since pigmented chromatophores play a key role in cephalopod color change, we also measured the spectral reflectance of individual cuttlefish chromatophores under the microscope, and confirm the results from a previous publication reporting three distinct colors of chromatophores (yellow, orange, and dark brown) on the animals’ dorsal side. Taken together, our results show that the color variations in substrate and animal skin can be very similar and that this may facilitate color match on natural substrates in the absence of color vision.

Plagioclase preferred orientation in layered mylonites: Evaluation of flow laws for the lower crust

Luc Mehl — 2008-06-11T18:13:30-00:00

Journal of Geophysical Research, Vol. 113 (7 May 2008), B05202.

We evaluate the applicability of plagioclase and gabbro flow laws by comparing predicted and observed deformation mechanisms in gabbroic shear zones. Gabbros and layered gabbro mylonites were collected from the Southwest Indian Ridge (SWIR), Ocean Drilling Program Hole 735B. Deformation temperatures are constrained by two-pyroxene thermometry, stress is estimated from grain size, and deformation mechanisms are analyzed by microstructure and the presence or absence of a lattice preferred orientation (LPO). Our analyses indicate that mylonite layers deformed at a strain rate in the range of 10−12 to 10−11 s−1, while coarse-grained gabbro deformed at a strain rate of approximately 10−14 to 10−13 s−1. Plagioclase in pure plagioclase mylonite layers exhibit strong LPOs indicating that they deformed by dislocation creep. Plagioclase grain size in mixed plagioclase-pyroxene mylonite layers is finer than in pure plagioclase layers and depends on the size and proportion of pyroxenes. Progressive mixing of pyroxene and plagioclase within gabbro mylonite layers is accompanied by weakening of the LPO, indicating that phase mixing promotes a transition to diffusion creep processes that involve grain boundary sliding. Our results indicate that experimental flow laws are accurate at geologic strain rates, although the strain rate for diffusion creep of fine-grained gabbro may be underestimated. At the conditions estimated for the SWIR crust, our calculations suggest that strain localization leads to a factor of 2–4 decrease in lower crustal viscosity. Away from shear zones, the viscosity of lower gabbroic crust is predicted to be similar to that of dry upper mantle.

A mechanistic model of mid-latitude decadal climate variability

S Kravtsov — 2008-06-11T18:12:38-00:00

Physica D: Nonlinear Phenomena, Vol. 237, No. 5. (1 May 2008), pp. 584-599.

A simple heuristic model of coupled decadal ocean-atmosphere modes in middle latitudes is developed. Previous studies have treated atmospheric intrinsic variability as a linear stochastic process modified by a deterministic coupling to the ocean. The present paper takes an alternative view: based on observational, as well as process modeling results, it represents this variability in terms of irregular transitions between two anomalously persistent, high-latitude and low-latitude jet-stream states. Atmospheric behavior is thus governed by an equation analogous to that describing the trajectory of a particle in a double-well potential, subject to stochastic forcing. Oceanic adjustment to a positional shift in the atmospheric jet involves persistent circulation anomalies maintained by the action of baroclinic eddies; this process is parameterized in the model as a delayed oceanic response. The associated sea-surface temperature anomalies provide heat fluxes that affect atmospheric circulation by modifying the shape of the double-well potential. If the latter coupling is strong enough, the model's spectrum exhibits a peak at a periodicity related to the ocean's eddy-driven adjustment time. A nearly analytical approximation of the coupled model is used to study the sensitivity of this behavior to key model parameters.

Compound-specific radiocarbon dating of Ross Sea sediments: A prospect for constructing chronologies in high-latitude oceanic sediments

Naohiko Ohkouchi — 2008-06-11T18:11:46-00:00

Quaternary Geochronology, Vol. 3, No. 3. (August 2008), pp. 235-243.

We present an overview of the problems relating to the development of sedimentary chronologies for Antarctic margin sediments, and review the recent application of compound-specific radiocarbon dating methods for resolving them. Radiocarbon dating of solvent-extractable, short-chain (C14, C16, and C18) fatty acids isolated from surface sediments of the Ross Sea, Antarctica, revealed their ages to be consistent with that of the modern dissolved inorganic carbon (DIC) reservoir age (pre-bomb, [Delta]14C[approximate]-150[per mille sign]; post-bomb, [Delta]14C[approximate]-100[per mille sign]) in this region. This contrasts sharply with the radiocarbon ages of bulk organic matter in the corresponding sediments are substantially older ([Delta]14C=-298[per mille sign] to -712[per mille sign]). Furthermore, the radiocarbon ages of these fatty acids progressively increase with the core depth. These results clearly show a utility of the compound-specific radiocarbon dating for developing sediment chronologies in the Antarctic margin sediments. This approach is potentially applicable to Arctic Ocean, as well as other areas of Southern Ocean where similar interferences by fossil or pre-aged carbon inputs have hindered the progress in the development of late Quaternary paleoceanographic records.

Fluxes of CH4, CO2, NO, and N2O in an improved fallow agroforestry system in eastern Amazonia

Louis Verchot — 2008-06-11T18:10:48-00:00

Agriculture, Ecosystems & Environment, Vol. 126, No. 1-2. (June 2008), pp. 113-121.

The objective of this study was to evaluate the effect of leguminous fallows on methane (CH4), carbon dioxide (CO2), N oxides (N2O and NO) fluxes. We measured CH4, N2O, NO, and CO2 fluxes from improved fallows of Inga edulis and Acacia mangium during two successive fallow periods in an old agricultural frontier on sandy soils in eastern Amazonia. Sampling for the first fallow period was done in 1996 and 1997 while that for the second fallow was done in 1999 and 2000. We observed net CH4 uptake during majority of the sampling campaigns. We did not observe any significant difference in CH4 flux between improved fallows and unimproved fallows (control) during either of the sampling periods (P > 0.05). We observed significantly higher uptake during the dry season relative to wet season, indicating the importance of soil water content and gas transport on CH4 fluxes. For both wet and dry seasons, soil respiration rates (CO2), N2O and NO fluxes were similar for improved fallow plots and the control (P > 0.05). We did not observe any significant seasonality in soil respiration or NO fluxes, but there was a significant difference in N2O flux between seasons (P = 0.0638). Contrary to other studies, our observations suggest that improved fallows using N-fixing trees do not appear to decrease the soil CH4 sink and also do not seem to increase CO2 and N-oxide emission in these sandy Amazonian soils. The result for N oxides is particularly pertinent to greenhouse gas (GHG) accounting methods that assess N2O emissions as a fraction of N fixation.

Density currents in the Chicago River: Characterization, effects on water quality, and potential sources

Ryan Jackson — 2008-06-11T18:09:31-00:00

Science of The Total Environment, Vol. 401, No. 1-3. (15 August 2008), pp. 130-143.

Bidirectional flows in a river system can occur under stratified flow conditions and in addition to creating significant errors in discharge estimates, the upstream propagating currents are capable of transporting contaminants and affecting water quality. Detailed field observations of bidirectional flows were made in the Chicago River in Chicago, Illinois in the winter of 2005-06. Using multiple acoustic Doppler current profilers simultaneously with a water-quality profiler, the formation of upstream propagating density currents within the Chicago River both as an underflow and an overflow was observed on three occasions. Density differences driving the flow primarily arise from salinity differences between intersecting branches of the Chicago River, whereas water temperature is secondary in the creation of these currents. Deicing salts appear to be the primary source of salinity in the North Branch of the Chicago River, entering the waterway through direct runoff and effluent from a wastewater-treatment plant in a large metropolitan area primarily served by combined sewers. Water-quality assessments of the Chicago River may underestimate (or overestimate) the impairment of the river because standard water-quality monitoring practices do not account for density-driven underflows (or overflows). Chloride concentrations near the riverbed can significantly exceed concentrations at the river surface during underflows indicating that full-depth parameter profiles are necessary for accurate water-quality assessments in urban environments where application of deicing salt is common.

Climate-induced interannual variability of marine primary and export production in three global coupled climate carbon cycle models

B Schneider — 2008-06-09T16:49:47-00:00

Biogeosciences, Vol. 5, No. 2. (2008), pp. 597-614.

Fully coupled climate carbon cycle models are sophisticated tools that are used to predict future climate change and its impact on the land and ocean carbon cycles. These models should be able to adequately represent natural variability, requiring model validation by observations. The present study focuses on the ocean carbon cycle component, in particular the spatial and temporal variability in net primary productivity (PP) and export production (EP) of particulate organic carbon (POC). Results from three coupled climate carbon cycle models (IPSL, MPIM, NCAR) are compared with observation-based estimates derived from satellite measurements of ocean colour and results from inverse modelling (data assimilation). Satellite observations of ocean colour have shown that temporal variability of PP on the global scale is largely dominated by the permanently stratified, low-latitude ocean (Behrenfeld et al., 2006) with stronger stratification (higher sea surface temperature; SST) being associated with negative PP anomalies. Results from all three coupled models confirm the role of the low-latitude, permanently stratified ocean for anomalies in globally integrated PP, but only one model (IPSL) also reproduces the inverse relationship between stratification (SST) and PP. An adequate representation of iron and macronutrient co-limitation of phytoplankton growth in the tropical ocean has shown to be the crucial mechanism determining the capability of the models to reproduce observed interactions between climate and PP.

The impact on atmospheric CO2 of iron fertilization induced changes in the ocean's biological pump

X Jin — 2008-06-09T16:48:08-00:00

Biogeosciences, Vol. 5, No. 2. (2008), pp. 385-406.

Using numerical simulations, we quantify the impact of changes in the ocean's biological pump on the air-sea balance of CO2 by fertilizing a small surface patch in the high-nutrient, low-chlorophyll region of the eastern tropical Pacific with iron. Decade-long fertilization experiments are conducted in a basin-scale, eddy-permitting coupled physical/biogeochemical/ecological model. In contrast to previous studies, we find that most of the dissolved inorganic carbon (DIC) removed from the euphotic zone by the enhanced biological export is replaced by uptake of CO2 from the atmosphere. Atmospheric uptake efficiencies, the ratio of the perturbation in air-sea CO2 flux to the perturbation in export flux across 100 m, integrated over 10 years, are 0.75 to 0.93 in our patch size-scale experiments. The atmospheric uptake efficiency is insensitive to the duration of the experiment. The primary factor controlling the atmospheric uptake efficiency is the vertical distribution of the enhanced biological production and export. Iron fertilization at the surface tends to induce production anomalies primarily near the surface, leading to high efficiencies. In contrast, mechanisms that induce deep production anomalies (e.g. altered light availability) tend to have a low uptake efficiency, since most of the removed DIC is replaced by lateral and vertical transport and mixing. Despite high atmospheric uptake efficiencies, patch-scale iron fertilization of the ocean's biological pump tends to remove little CO2 from the atmosphere over the decadal timescale considered here.

A Visual Basic program to plot sediment grain-size data on ternary diagrams

LJ Poppe — 2008-06-09T16:45:00-00:00

Computers & Geosciences, Vol. 34, No. 5. (May 2008), pp. 561-565.

Cell-specific beta-N-acetylglucosaminidase activity in cultures and field populations of eukaryotic marine phytoplankton

Alena Strojsova — 2008-06-09T16:43:47-00:00

FEMS Microbiology Ecology, Vol. 64, No. 3. (2008), pp. 351-361.

Abstract It is widely appreciated that eukaryotic marine phytoplankton can hydrolyze a variety of compounds within the dissolved organic matter (DOM) pool in marine environments. Herein, cultures and field populations of marine phytoplankton were assayed for beta-N-acetylglucosaminidase activity, a terminal enzyme of chitin degradation. A traditional bulk assay, which can assess hydrolytic rate, but is not cell-specific, was complemented with a cell-specific assay that images the activity associated with single cells using an enzyme labeled fluorescence (ELF) substrate. beta-N-acetylglucosaminidase activity was widespread across various taxa of marine phytoplankton, and activity was observed both under controlled culture conditions and in field populations. The number of cells with enzyme activity varied with the nutritional physiology of the test species in three of the 17 cultures tested. In these three cases the number of cells with activity in the low nutrient medium was higher than in nutrient replete medium. Taken together, these data suggest that a broad group of marine phytoplankton may be a relevant part of chitin-like DOM degradation and should be incorporated into conceptual models of chitin cycling in marine systems.

Evolving east Asian river systems reconstructed by trace element and Pb and Nd isotope variations in modern and ancient Red River-Song Hong sediments

Peter Clift — 2008-05-03T13:45:49-00:00

Geochemistry Geophysics Geosystems, Vol. 9 (30 April 2008), Q04039.

Rivers in east Asia have been recognized as having unusual geometries, suggestive of drainage reorganization linked to Tibetan Plateau surface uplift. In this study we applied a series of major and trace element proxies, together with bulk Nd and single K-feldspar grain Pb isotope ion probe isotope analyses, to understand the sediment budget of the modern Red River. We also investigate how this may have evolved during the Cenozoic. We show that while most of the modern sediment is generated by physical erosion in the upper reaches in Yunnan there is significant additional flux from the Song Lo, draining Cathaysia and the SW Yangtze Block. Nd isotope data suggest that 40% of the modern delta sediment comes from the Song Lo. Carbonates in the Song Lo basin make this a major control on the Red River Sr budget. Erosion is not a simple function of monsoon precipitation. Active rock uplift is also required to drive strong erosion. Single grain Pb data show a connection in the Eocene between the middle Yangtze and the Red River, and probably with rivers draining the Songpan Garze terrane. However, the isotope data do not support a former connection with the upper Yangtze, Mekong, or Salween rivers. Drainage capture appears to have occurred throughout the Cenozoic, consistent with surface uplift propagating gradually to the southeast. The middle Yangtze was lost from the Red River prior to 24 Ma, while the connection to the Songpan Garze was cut prior to 12 Ma. The Song Lo joined the Red River after 9 Ma. Bulk sample Pb analyses have limited provenance use compared to single grain data, and detailed provenance is only possible with a matrix of different proxies.

Mixing across the Arctic Ocean: Microstructure observations during the Beringia 2005 Expedition

Luc Rainville — 2008-06-09T16:40:25-00:00

Geophysical Research Letters, Vol. 35 (30 April 2008), L08606.

Turbulent-scale temperature and conductivity were measured during the pan-arctic Beringia 2005 Expedition. The rates of dissipation of thermal variance and diapycnal diffusivities are calculated along a section from Alaska to the North Pole, across deep flat basins (Canada and Makarov Basins) and steep ridges (Alpha-Mendeleev and Lomonosov Ridges). The mixing rates are observed to be small relative to lower latitudes but also remarkably non-uniform. Relatively elevated turbulence is found over deep topography, confirming the dominant role of bottom-generated internal waves. Measured patterns of mixing in the Arctic are also associated with other mechanisms, such as double-diffusive structures and deep overflows. A better knowledge of the distribution of mixing is essential to understand the dynamics of the changing Arctic environment.

Ancient DNA fragments inside Classical Greek amphoras reveal cargo of 2400-year-old shipwreck

Maria Hansson — 2008-06-09T16:39:45-00:00

Journal of Archaeological Science, Vol. 35, No. 5. (May 2008), pp. 1169-1176.

The origins and spread of eastern Mediterranean civilizations 4000-2000 years ago constitute defining events in human development. Interregional connections across the sea played critical roles in building increasingly sophisticated economies and societies. Research of trade and exchange among these first centers has relied upon ancient societies' archaeological artifacts. The most ubiquitous artifacts recovered from shipwreck sites are ceramic transport jars, amphoras. However, for archaeologists and historians determining the original contents of these containers has been problematic, aided only occasionally by physical evidence (e.g. olive pits, resins) found inside excavated jars. Here, we investigate whether modern DNA analyses can reveal original contents of amphoras containing no visible physical remains. Using chloroplast DNA markers and PCR we analyzed the walls of two amphoras recovered from a 2400 year-old shipwreck off the Greek island of Chios. Our results show that short (<=100 bp) ancient DNA fragments can be extracted from scrapings taken from amphoras' interior walls. These DNA fragments identify the amphoras' original contents. Our analyses indicate that one of the amphoras most likely contained olive oil and oregano, even though no physical traces of remains are visible inside the jar. The second amphora might have contained mastic resin; resins of various types were preservatives commonly added to ancient wine. Our analyses are the first to demonstrate that ancient DNA fragments can be extracted from the walls of amphoras recovered from underwater shipwreck sites. This opens a new field of molecular archaeology analyses, and provides a powerful tool for obtaining information about the agricultural production, contact networks, and economies of the early civilizations.

Late Archean to Early Proterozoic lithospheric mantle beneath the western North China craton: Sr-Nd-Os isotopes of peridotite xenoliths from Yangyuan and Fansi

Yi-Gang Xu — 2008-06-09T16:38:41-00:00

Lithos, Vol. 102, No. 1-2. (April 2008), pp. 25-42.

Sr-Nd-Os isotopic analyses are presented for peridotite xenoliths from Tertiary alkali basalts in Yangyuan and Fansi with the aim of identifying and characterizing the relics of ancient lithospheric mantle that survived lithospheric removal in the western North China Craton (NCC). The analyzed samples are residual lherzolites and harzburgites, ranging from fertile to highly depleted (0.36-4.0 wt% Al2O3) composition. Some LREE-enriched samples are characterized by moderate 87Sr/86Sr (0.7044 to 0.7047) and low [epsilon]Nd (- 6.9 to - 10.6), pointing to an EMI-type signature. This is distinct from the predominant depleted isotopic composition in mantle xenoliths from eastern China. Os isotopic ratios range from 0.1106 to 0.1325. The lower limit is the most unradiogenic value measured so far for Cenozoic basalt-borne xenoliths from eastern China. Two samples show radiogenic Os ratios higher than that of the primitive upper mantle, one sample has an anomalously high Os concentration (> 9 ppb). These samples also show high La/Yb, consistent with the addition of radiogenic components during the infiltration of asthenosphere-derived and/or subduction-related melts in the lithospheric mantle. The remaining samples define positive correlations between 187Os/188Os and indices of melt extraction, which yield a model age of ~ 2.6 Ga. This age of melt extraction overlaps with the Nd model age of the overlying crust, indicating a coupled crust-mantle system in the western NCC. This contrasts with the decoupled nature in the eastern NCC, suggesting distinct mantle domains underneath the NCC. Such a heterogeneous age structure of the upper mantle is compatible with the view that the lithospheric removal was largely limited to the eastern NCC.

The benefits of rationalization: The case of the American lobster fishery.

SR Steinback — 2008-06-09T16:37:53-00:00

Marine Resource Economics, Vol. 23, No. 1. (2008), pp. 37-63.

Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within [`]Amoebozoa' upon removal of varying rate classes of SSU-rDNA

Yonas Tekle — 2008-06-01T22:32:21-00:00

Molecular Phylogenetics and Evolution, Vol. 47, No. 1. (April 2008), pp. 339-352.

Placing amoeboid lineages on the eukaryotic tree of life is difficult due to the paucity of comparable morphological characters and the limited molecular data available for many groups. This situation has led to the lumping of distantly related lineages into large inclusive groups, such as Sarcodina, that do not reflect evolutionary relationships. Previous analyses of molecular markers with limited taxon sampling reveal members of Sarcodina are scattered in five of the six proposed supergroups. We have used multigene analyses to place seven diverse amoeboid lineages--two Nolandella spp., Rhizamoeba sp., Pessonella sp., Arcella hemisphaerica, Arachnula sp. and Trichosphaerium sp.--on the eukaryotic tree of life. Bayesian analysis of the concatenated data of the four genes sequenced (SSU-rDNA, actin, alpha-tubulin and beta-tubulin), including diverse representatives of eukaryotes, indicates that all seven taxa group within the [`]Amoebozoa' supergroup. We further performed separate analyses of the well-sampled SSU-rDNA and actin genes using Bayesian and Maximum Likelihood analyses to assess the positions of our newly characterized taxa. In the case of SSU-rDNA, we performed extensive analyses with removal of the fastest rates classes to evaluate the stability and resolution of various taxonomic hypotheses within [`]Amoebozoa'. Five of our seven amoeboid lineages fall within well-supported clades that are corroborated by morphology. In contrast, the positions of Arachnula sp. and Trichosphaerium sp. in the SSU-rDNA gene trees are unstable and vary by analyses. Placement of these taxa will require additional data from slowly evolving genes combined with taxon-rich phylogenetic analyses. Finally, the analyses without the fastest rate classes demonstrate that SSU-rDNA has a limited signal for deep relationships within the [`]Amoebozoa'.

In the squid axon Na+/Ca2+ exchanger the state of the Cai-regulatory site influences the affinities of the intra- and extracellular transport sites for Na+ and Ca2+

Reinaldo Dipolo — 2008-06-09T16:32:50-00:00

Pflügers Archiv European Journal of Physiology, Vol. 456, No. 3. (1 June 2008), pp. 623-633.

In squid axons, intracellular Mg2+ reduces the activity of the Na+/Ca2+ exchanger by competing with $$\textCa_\texti^\text2 + $$ for its regulatory site. The state of the Cai-regulatory site (active–inactive) also alters the apparent affinity of intra- and extracellular transport sites. Conditions that hinder the binding of $$\textCa_\texti^\text2 + $$ (low pHi, low [Ca2+]i, high [Mg2+]i) diminish the apparent affinity of intracellular transport sites, in particular for Nai due to its synergism with H+ inhibition, but less noticeably for $$\textCa_\texti^\text2 + $$ because of its antagonism towards ($$\textH_\texti^\text + \text + Na_\texti^\text + $$) and $$\textMg_\texti^\text2 + $$ inhibitions. These are kinetic effects unrelated to the true affinity of the sites. With the Cai-regulatory site saturated, the intracellular transporting sites are insensitive to [H+]i and to ATP. Likewise, the state of the Cai-regulatory site (activated or inactivated) influences the affinity of the extracellular Cao and Nao-transport sites (trans effects). In this case, the effects are opposite to those predicted by any of the transport schemes proposed for the Na+/Ca2+exchanger; i.e. its mechanism remains unexplained. In addition to their intrinsic importance for a full understanding of the properties of the Na+/Ca2+ exchanger, these findings show a new way by which the state of the Cai-regulatory site may determine net movements of Ca2+ through this system.

On the history of meridional overturning circulation schematic diagrams

Philip Richardson — 2008-06-09T16:32:09-00:00

Progress In Oceanography, Vol. 76, No. 4. (March 2008), pp. 466-486.

Recent global warming caused by humans and the prediction of a reduced Atlantic Ocean meridional overturning circulation in the future has increased interest in the role of the overturning circulation in climate change. A schematic diagram of the overturning circulation called the "Great Ocean Conveyor Belt," published by Wallace Broecker in 1987, has become a popular image that emphasizes the inter-connected ocean circulation and the northward flux of heat in the Atlantic. This seems a good time to review the development of the conveyor belt concept and summarize the history of overturning circulation schematics. In the 19th century it was thought that symmetric overturning circulation cells were located on either side of the equator in the Atlantic. As new hydrographic measurements were obtained, circulation schematics in the early 20th century began to show the inter-hemispheric overturning circulation in the Atlantic. In the second half of the 20th century schematics showed the global ocean overturning circulation including connections between the Atlantic and the Pacific and Indian Oceans. Some recent schematics of the overturning circulation show its complexities, but as more information is included these schematics have also become complex and not as easy to understand as the simple Broecker 1987 version. However, these complex schematics, especially the quantitative ones, represent valuable syntheses of our developing knowledge of the overturning circulation.

Particulate organic carbon fluxes to the ocean interior and factors controlling the biological pump: A synthesis of global sediment trap programs since 1983

Susumu Honjo — 2008-06-09T16:31:06-00:00

Progress In Oceanography, Vol. 76, No. 3. (March 2008), pp. 217-285.

Particulate organic carbon (POC) is vertically transported to the oceanic interior by aggregates and their ballasts, mainly CaCO3 and biogenic opal, with a smaller role for lithogenic aerosols through the mesopelagic zone. Diel migrating zooplankton communities effect vertical transport and remineralization of POC in the upper layers of the ocean. Below 1.5 km, the presence of zooplankton is reduced and thus the aggregates travel mainly by gravitational transport. We normalized the fluxes of POC, CaCO3, and biogenic opal from data published on samples collected at 134 globally distributed, bottom-tethered, time-series sediment trap (TS-trap) stations to annual mole fluxes at the mesopelagic/bathypelagic boundary (m/b) at 2 km and defined them as Fm/bCorg, Fm/bCinorg, and Fm/bSibio. Using this global data set, we investigated (1) the geographic contrasts of POC export at m/b and (2) the supply rate of [summation operator]CO2 to the world mesopelagic water column. Fm/bCorg varies from 25 (Pacific Warm Pool) to 605 (divergent Arabian Sea) mmolC m-2 yr-1; Fm/bCinorg varies from >8 (high latitude Polar Oceans) or 15 (Pacific Warm Pool) to 459 (divergent Arabian Sea) mmolC m-2 yr-1; and Fm/bSibio, the most spatially/temporally variable flux, ranges from 6 (North Atlantic Drift) to 1118 (Pacific Subarctic Gyre) mmolSi m-2 yr-1. The oceanic region exhibiting the highest POC flux over a significantly large region is the area of the North Pacific Boreal Gyres where the average Fm/bCorg = 213, Fm/bCinorg = 126, and Fm/bSibio = 578 mmol m-2 yr-1. Fm/bCorg and Fm/bCinorg are particularly high in large upwelling margins, including the divergent Arabian Sea and off Cape Verde. One of the data sets showing the lowest flux over a significant region/basin is Fm/bCorg = 39, Fm/bCinorg = 69, and Fm/bSibio = 22 mmol m-2 yr-1 in the North Pacific subtropical/tropical gyres; Pan-Atlantic average fluxes are similar except Fm/bSibio fluxes are even lower. Where Corg/Cinorg and Sibio/Cinorg are <1 defines the "Carbonate Ocean", and where these ratios are [greater-or-equal, slanted]1 defines the "Silica Ocean". The Carbonate Ocean occupies about 80% of the present world pelagic ocean between the two major oceanographic fronts, the North Pacific Polar Front and the Antarctic Polar Front, and the Silica Ocean is found on the polar sides of these fronts. The total global annual fluxes of Fm/bCorg, Fm/bCinorg, and Fm/bSibio at m/b calculated by parameterizations of the export flux data from 134 stations are surprisingly similar; 36.2, 33.8, and 34.6 teramol yr-1 (120, 112, and 114 mmol m-2 yr-1), respectively, resulting in a near uniform binary ratio between the above three elements of about one. The global ternary % ratios estimated from 152 TS-trap samples of the three elements are 35:32:33. From our global Fm/bCorg and a published model estimate of the global export production, we estimate the regeneration rate of CO2 through the mesopelagic zone by the biological pump is 441 teramolC yr-1. Based on our global Fm/bCinorg and recently estimated global primary production of PIC, 36-86 teramolC yr-1 of PIC is assumed to be dissolved within the upper 2 km of the water column.

Atypical properties of a conventional calcium channel beta subunit from the platyhelminth Schistosoma mansoni

Vicenta Salvador-Recatala — 2008-03-27T06:01:43-00:00

BMC Physiology, Vol. 8 (26 March 2008), 6.

Background: The function of voltage-gated calcium (Cav) channels greatly depends on coupling to cytoplasmic accessory β subunits, which not only promote surface expression, but also modulate gating and kinetic properties of the α1 subunit. Schistosomes, parasitic platyhelminths that cause schistosomiasis, express two β subunit subtypes: a structurally conventional β subunit and a variant β subunit with unusual functional properties. We have previously characterized the functional properties of the variant Cavβ subunit. Here, we focus on the modulatory phenotype of the conventional Cavβ subunit (SmCavβ) using the human Cav2.3 channel as the substrate for SmCavβ and the whole-cell patch-clamp technique. Results: The conventional Schistosoma mansoni Cavβ subunit markedly increases Cav2.3 currents, slows macroscopic inactivation and shifts steady state inactivation in the hyperpolarizing direction. However, currents produced by Cav2.3 in the presence of SmCavβ run-down to approximately 75% of their initial amplitudes within two minutes of establishing the whole-cell configuration. This suppressive effect was independent of Ca2+, but dependent on intracellular Mg2+-ATP. Additional experiments revealed that SmCavβ lends the Cav2.3/SmCavβ complex sensitivity to Na+ ions. A mutant version of the Cavβ subunit lacking the first forty-six amino acids, including a string of twenty-two acidic residues, no longer conferred sensitivity to intracellular Mg2+-ATP and Na+ ions, while continuing to show wild type modulation of current amplitude and inactivation of Cav2.3. Conclusion: The data presented in this article provide insights into novel mechanisms employed by platyhelminth Cavβ subunits to modulate voltage-gated Ca2+ currents that indicate interactions between the Ca2+ channel complex and chelated forms of ATP as well as Na+ ions. These results have potentially important implications for understanding previously unknown mechanisms by which platyhelminths and perhaps other organisms modulate Ca2+ currents in excitable cells.

Exploring historical trends using taxonomic name metadata

Indra Sarkar — 2008-05-14T13:56:28-00:00

BMC Evolutionary Biology, Vol. 8 (13 May 2008), 144.

Background: Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy. Results: From the over 10.7 million taxonomic names that are part of the uBio system [4], approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pipe-delimited file was then generated, organized according to a Linnaean hierarchy and by years from 1750 to 2004, and imported into an Excel workbook. A series of macros were developed to create an Excel-based tool and a complementary Web site to explore the taxonomic data. A cursory and speculative analysis of the data reveals observable trends that may be attributable to significant events that are of both taxonomic (e.g., publishing of key monographs) and societal importance (e.g., world wars). The findings also help quantify the number of taxonomic descriptions that may be made available through digitization initiatives. Conclusion: Temporal organization of taxonomic data can be used to identify interesting biological epochs relative to historically significant events and ongoing efforts. We have developed an Excel workbook and complementary Web site that enables one to explore taxonomic trends for Linnaean taxonomic groupings, from Kingdoms to Families.

Sulfur isotope evidence for microbial sulfate reduction in altered oceanic basalts at ODP Site 801

Olivier Rouxel — 2008-05-21T12:37:00-00:00

Earth and Planetary Science Letters, Vol. 268, No. 1-2. (15 April 2008), pp. 110-123.

The subsurface biosphere in the basaltic ocean crust is potentially of major importance in affecting chemical exchange between the ocean and lithosphere. Alteration of the oceanic crust commonly yields secondary pyrite that is depleted in 34S relative to igneous sulfides. Although these 34S depleted sulfur isotope ratios may point to signatures of biological fractionation, previous interpretations of sulfur isotope fractionation in altered volcanic rocks have relied on abiotic fractionation processes between intermediate sulfur species formed during basalt alteration. Here, we report results for multiple S-isotope (32S, 33S, 34S) compositions of altered basalts at ODP Site 801 in the western Pacific and provide evidence for microbial sulfate reduction within the volcanic oceanic crust. In-situ ion-microprobe analyses of secondary pyrite in basement rocks show a large range of [delta]34S values, between - 45[per mille sign] and 1[per mille sign], whereas bulk rock [delta]34S analyses yield a more restricted range of - 15.8 to 0.9[per mille sign]. These low and variable [delta]34S values, together with bulk rock S concentrations ranging from 0.02% up to 1.28% are consistent with loss of magmatic primary mono-sulfide and addition of secondary sulfide via microbial sulfate reduction. High-precision multiple sulfur-isotope (32S/33S/34S) analyses suggest that secondary sulfides exhibit mass-dependent equilibrium fractionation relative to seawater sulfate in both [delta]33S and [delta]34S values. These relationships are explained by bacterial sulfate reduction proceeding at very low metabolic rates. The determination of the S-isotope composition of bulk altered oceanic crust demonstrates that S-based metabolic activity of subsurface life in oceanic basalt is widespread, and can affect the global S budget at the crust-seawater interface.

Appearance of new tetraspanin genes during vertebrate evolution

Antonio Garcia-España — 2008-05-21T12:35:16-00:00

Genomics, Vol. 91, No. 4. (April 2008), pp. 326-334.

A detailed phylogenetic analysis of tetraspanins from 10 fully sequenced metazoan genomes and several fungal and protist genomes gives insight into their evolutionary origins and organization. Our analysis suggests that the superfamily can be divided into four large families. These four families-the CD family, CD63 family, uroplakin family, and RDS family-are further classified as consisting of several ortholog groups. The clustering of several ortholog groups together, such as the CD9/Tsp2/CD81 cluster, suggests functional relatedness of those ortholog groups. The fact that our studies are based on whole genome analysis enabled us to estimate not only the phylogenetic relationships among the tetraspanins, but also the first appearance in the tree of life of certain tetraspanin ortholog groups. Taken together, our data suggest that the tetraspanins are derived from a single (or a few) ancestral gene(s) through sequence divergence, rather than convergence, and that the majority of tetraspanins found in the human genome are vertebrate (21 instances), tetrapod (4 instances), or mammalian (6 instances) inventions.

Top-down and bottom-up control of infauna varies across the saltmarsh landscape

JW Fleeger — 2008-05-21T12:34:13-00:00

Journal of Experimental Marine Biology and Ecology, Vol. 357, No. 1. (17 March 2008), pp. 20-34.

Responses of infaunal saltmarsh benthic invertebrates to whole-ecosystem fertilization and predator removal were quantified in Plum Island Estuary, Massachusetts, USA. Throughout a growing season, we enriched an experimental creek on each flooding tide to 70 [mu]M NO3- and 4 [mu]M PO4- 3 (a 10× increase in loading above background), and we reduced Fundulus heteroclitus density by 60% in a branch of the fertilized and a reference creek. Macroinfauna and meiofauna were sampled in creek (mudflat and creek wall), marsh edge (tall-form Spartina alterniflora) and marsh platform (Spartina patens and stunted S. alterniflora) habitats before and after treatments were begun; responses were tested with BACI-design statistics. Treatment effects were most common in the mid-range of the inundation gradient. Most fertilization effects were on creek wall where ostracod abundance increased, indices of copepod reproduction increased and copepod and annelid communities were altered. These taxa may use epiphytes (that respond rapidly to fertilization) of filamentous algae as a food source. Killifish reduction effects on meiobenthic copepod abundance were detected at the marsh edge and suggest predator limitation. Fish reduction effects on annelids did not suggest top-down regulation in any habitat; however, fish reduction may have stimulated an increased predation rate on annelids by grass shrimp. Interactions between fertilization and fish reduction occurred under S. patens canopy where indirect predator reduction effects on annelids were indicated. No effects were observed in mudflat or stunted S. alterniflora habitats. Although the responses of infauna to fertilization and predator removal were largely independent and of similar mild intensity, our data suggests that the effects of ecological stressors vary across the marsh landscape.

Factors Affecting Catch-and-Release Mortality of Bluefish

Mary Fabrizio — 2008-05-21T12:30:58-00:00

North American Journal of Fisheries Management, Vol. 28, No. 2. (2008), pp. 533-546.

Recreational harvests of bluefish Pomatomus saltatrix along the U.S. coast from Maine to Florida exceed commercial harvests, and in recent years about 60–70% of angler-captured fish are released alive. The proportion of fish that survive hooking, handling, and release back to the ocean is unknown; however, if catch-and-release mortality is high, it may represent a significant component of the overall bluefish mortality rate. We estimated long-term (21-d) hooking mortality rates of field-captured bluefish and investigated the effects of various factors on postrelease mortality. Age, length, and the occurrence of bleeding were significant factors associated with catch-and-release mortality, which we estimated to be 38.8%. About 65% of the mortality was initial mortality, and the remainder was delayed mortality. We also performed a laboratory study to examine the physiological response of bluefish to two independent processes (hooking and release versus transfer in coolers to the laboratory) relevant to the field study. Laboratory-held fish that were hooked and released exhibited elevated concentrations of potassium in their blood, suggesting that they experienced either an osmotic imbalance or cellular damage. Laboratory-held fish exposed to the transfer treatment only exhibited osmotic imbalance (elevated plasma sodium concentration) and evidence of anaerobic metabolism (elevated plasma lactate concentration). Our findings indicate that bluefish age and size contribute to variable levels of metabolic stress and that delayed postrelease mortality is considerable.

Possible evidence for wet Heinrich phases in tropical NE Australia: the Lynch's Crater deposit

Joanne Muller — 2008-05-21T12:28:38-00:00

Quaternary Science Reviews, Vol. 27, No. 5-6. (March 2008), pp. 468-475.

Unarguably, one of the most significant paleoclimatological discoveries of the last two decades has been that of abrupt climate events (Dansgaard-Oeschger cycles and Heinrich events). Most evidence for these events has originated from the high-latitude Northern Hemisphere, with few records documenting the response of the low latitude Southern Hemisphere. Here we present new data from Lynch's Crater, a unique terrestrial record from NE-Australia that may show evidence for southward propagations of the Intertropical Convergence Zone (ITCZ) during abrupt climate perturbations as a result of alteration of the low latitude air masses. Proxies for precipitation/wetness indicate enhanced rainfall in the region during Heinrich events (H events 1-3) and the 8.2 ka Northern Hemisphere cold event. A fully coupled atmosphere/ocean climate model simulating a 1 Sv freshwater influx to the North Atlantic Ocean produces a scenario which agrees with the climate changes shown by the Lynch's Crater record. The model shows precipitation anomalies that include a southward migration of the ITCZ and a zonal shift in mid-latitude storm tracks over the Southern Hemisphere equatorial region. These data indicate large-scale shifts of the austral summer ITCZ position that is known to control monsoonal precipitation in NE Australia. This terrestrial record from Australia may demonstrate the involvement of the tropical western Pacific Ocean in ITCZ migrations during abrupt climate events of the last glacial period. Defining such past migrations offers insight into the importance and role of the equatorial region in global climate dynamics.

Seasonal Speedup Along the Western Flank of the Greenland Ice Sheet

Ian Joughin — 2008-05-07T00:37:38-00:00

Science (17 April 2008), 1153288.

It has been widely hypothesized that a warmer climate in Greenland would increase the volume of lubricating surface-melt reaching the ice-bedrock interface, accelerating ice flow and increasing mass loss. We have assembled a dataset that provides a synoptic-scale view, spanning ice-sheet to outlet-glacier flow, with which to evaluate this hypothesis. On the ice sheet, these data reveal summer speedups (50-100%) consistent with, but somewhat larger than, earlier observations. The relative speedup of outlet glaciers, however, is far smaller (<15%). Furthermore, the dominant seasonal influence on Jakobshavn Isbrae's flow is the calving front's annual advance and retreat. With other effects producing outlet-glacier speedups an order of magnitude larger, seasonal melt's influence on ice flow is likely confined to those regions dominated by ice-sheet flow. 10.1126/science.1153288

An integrated greenhouse gas assessment of an alternative to slash-and-burn agriculture in eastern Amazonia

Eric Davidson — 2008-05-21T12:25:22-00:00

Global Change Biology, Vol. 14, No. 5. (2008), pp. 998-1007.

Fires set for slash-and-burn agriculture contribute to the current unsustainable accumulation of atmospheric greenhouse gases, and they also deplete the soil of essential nutrients, which compromises agricultural sustainability at local scales. Integrated assessments of greenhouse gas emissions have compared intensive cropping systems in industrialized countries, but such assessments have not been applied to common cropping systems of smallholder farmers in developing countries. We report an integrated assessment of greenhouse gas emissions in slash-and-burn agriculture and an alternative chop-and-mulch system in the Amazon Basin. The soil consumed atmospheric methane (CH4) under slash-and-burn treatment and became a net emitter of CH4 to the atmosphere under the mulch treatment. Mulching also caused about a 50 increase in soil emissions of nitric oxide and nitrous oxide and required greater use of fertilizer and fuel for farm machinery. Despite these significantly higher emissions of greenhouse gases during the cropping phase under the alternative chop-and-mulch system, calculated pyrogenic emissions in the slash-and-burn system were much larger, especially for CH4. The global warming potential CO2-equivalent emissions calculated for the entire crop cycles were at least five times lower in chop-and-mulch compared with slash-and-burn. The crop yields were similar for the two systems. While economic and logistical considerations remain to be worked out for alternatives to slash-and-burn, these results demonstrate a potential ‘win-win’ strategy for maintaining soil fertility and reducing net greenhouse gas emissions, thus simultaneously contributing to sustainability at both spatial scales.

Peroxisome Proliferation in Foraminifera Inhabiting the Chemocline: An Adaptation to Reactive Oxygen Species Exposure?

Joan Bernhard — 2008-05-05T14:26:48-00:00

Journal of Eukaryotic Microbiology, Vol. 55, No. 3. (June 2008), pp. 135-144.

Certain foraminiferal species are abundant within the chemocline of marine sediments. Ultrastructurally, most of these species possess numerous peroxisomes complexed with the endoplasmic reticulum (ER); mitochondria are often interspersed among these complexes. In the Santa Barbara Basin, pore-water bathing Foraminifera and co-occurring sulfur-oxidizing microbial mats had micromolar levels of hydrogen peroxide (H2O2), a reactive oxygen species that can be detrimental to biological membranes. Experimental results indicate that adenosine triphosphate concentrations are significantly higher in Foraminifera incubated in 16 μM H2O2 than in specimens incubated in the absence of H2O2. New ultrastructural and experimental observations, together with published results, lead us to propose that foraminiferans can utilize oxygen derived from the breakdown of environmentally and metabolically produced H2O2. Such a capability could explain foraminiferal adaptation to certain chemically inhospitable environments; it would also force us to reassess the role of protists in biogeochemistry, especially with respect to hydrogen and iron. The ecology of these protists also appears to be tightly linked to the sulfur cycle. Finally, given that some Foraminifera bearing peroxisome–ER complexes belong to evolutionarily basal groups, an early acquisition of the capability to use environmental H2O2 could have facilitated diversification of foraminiferans during the Neoproterozoic.

CDK13: A NEW POTENTIAL HIV-1 INHIBITORY FACTOR REGULATING VIRAL mRNA SPLICING

Reem Berro — 2008-05-21T12:23:31-00:00

J. Virol. (14 May 2008), JVI.02543-07.

The human immunodeficiency virus type 1 (HIV-1) Tat is a 14 kDa viral protein that acts as a potent transactivator by binding to TAR (transactivation-responsive region), a structured RNA element located at the 5' end of all HIV-1 transcripts. Tat transactivates viral gene expression by inducing the phosphorylation of the C-terminal domain (CTD) of RNA Pol II through several Tat-activated kinases and by recruiting chromatin remodeling complexes and histone modifying enzymes to the HIV-1 LTR. Histone acetyl-transferases (HATs), including p300 and hGCN5, not only acetylate histones but also acetylate Tat at lysine positions 50 and 51 in the arginine-rich motif (ARM). Acetylated Tat (AcTat) at positions 50 and 51 interacts with a specialized protein module, the bromodomain, and recruits novel factors having this particular domain such as P/CAF and SWI/SNF. Other than its effect on transcription, Tat has been shown to be involved in splicing. In this study, we demonstrate that Tat interacts with CDK13 both in vivo and in vitro. We also found that CDK13 increases HIV-1 mRNA splicing and favours the production of the doubly-spliced protein Nef. In addition, we demonstrate that CDK13 acts as a possible restriction factor, in that its overexpression decreases the production of the viral proteins Gag and Env and subsequently suppresses virus production. Using siRNA against CDK13, we show that silencing of CDK13 leads to a significant increase in virus production. Finally, we demonstrate that CDK13 mediates its effect on splicing through the phosphorylation of ASF/SF2. 10.1128/JVI.02543-07

Using δ15N to Assess Coupling between Watersheds and Estuaries in Temperate and Tropical Regions

Jennifer Bowen — 2008-05-21T12:22:57-00:00

Journal of Coastal Research, Vol. 24, No. 3. (2008), pp. 804-813.

Hydrological coupling between watersheds and estuaries is an important element in establishing eutrophic conditions in coastal waters. In coupled systems, nutrients derived on land enter estuaries through groundwater flow or stream runoff, resulting in increased rates of primary production. The extent of coupling is determined by precipitation, evapotransporation, and water use practices. We use stable nitrogen isotopes, salinity, and nutrient data to assess coupling in two temperate and two tropical ecosystems. In each region, we selected two estuaries, one pristine and one with considerable agricultural or urban development. In pristine systems freshwater entering estuaries had low nitrogen concentrations and low nitrogen isotopic signatures. In receiving waters of the pristine systems, there were similarly low nutrient concentrations, and the isotopic signatures in the estuary were similar to the signatures of incoming groundwater. In both disturbed sites freshwater on the watershed had high nitrogen concentrations and enriched nitrogen isotopic signatures. In the temperate system, the estuarine water had high nitrate concentrations and nitrogen isotopic signatures that were similar to that of the incoming freshwater, indicating that the watershed and estuary were tightly coupled. In contrast, in the disturbed tropical site the estuary had extremely low nitrogen concentrations, and the isotopic signatures were unrelated to the signatures found in freshwater on the adjoining watershed. These results demonstrate that under sufficiently dry conditions, watersheds and estuaries may be uncoupled.

Characterization of Cytochrome 579, an unusual cytochrome isolated from an iron oxidizing microbial community

Steven Singer — 2008-05-21T12:20:53-00:00

Appl. Environ. Microbiol. (9 May 2008), AEM.02799-07.

A novel, soluble cytochrome with an unusual visible spectral signature at 579 nm has been characterized after isolation from several different microbial biofilms collected in an extremely acidic ecosystem. Previous proteogenomic studies of a Fe(II)-oxidizing community indicated that this abundant red cytochrome could be extracted from the biofilms with dilute sulfuric acid. Here, we found that Fe(II)-dependent reduction of Cyt579 was thermodynamically favorable at pH>3, raising the possibility that Cyt579 acts as an accessory protein for electron transfer. Transmission electron microscopy of immuno-gold labeled biofilm indicated that the Cyt579 is localized near the bacterial cell surface, consistent with periplasmic localization. Further protein analysis of Cyt579, using preparative chromatofocusing and SDS-PAGE, revealed three forms of the protein that correspond to different N-terminal truncations of the amino acid sequence. Intact protein analysis corroborated the post-translational modifications of these forms and identified a genomically uncharacterized Cyt579 variant. Homology modeling was used to predict the overall cytochrome structure and heme binding site; positions of nine amino acid substitutions found in 3 Cyt579 variants all map to the surface of the protein and away from the heme group. Based on this detailed characterization of Cyt579, we propose that Cyt579 acts an electron transfer protein shuttling electrons derived from Fe(II) oxidation to support critical metabolic functions in the acidophilic microbial community. 10.1128/AEM.02799-07

Seabed mapping and characterization of sediment variability using the usSEABED data base

John Goff — 2008-05-14T19:55:59-00:00

Continental Shelf Research, Vol. 28, No. 4-5. (30 March 2008), pp. 614-633.

We present a methodology for statistical analysis of randomly located marine sediment point data, and apply it to the US continental shelf portions of usSEABED mean grain size records. The usSEABED database, like many modern, large environmental datasets, is heterogeneous and interdisciplinary. We statistically test the database as a source of mean grain size data, and from it provide a first examination of regional seafloor sediment variability across the entire US continental shelf. Data derived from laboratory analyses ("extracted") and from word-based descriptions ("parsed") are treated separately, and they are compared statistically and deterministically. Data records are selected for spatial analysis by their location within sample regions: polygonal areas defined in ArcGIS chosen by geography, water depth, and data sufficiency. We derive isotropic, binned semivariograms from the data, and invert these for estimates of noise variance, field variance, and decorrelation distance. The highly erratic nature of the semivariograms is a result both of the random locations of the data and of the high level of data uncertainty (noise). This decorrelates the data covariance matrix for the inversion, and largely prevents robust estimation of the fractal dimension. Our comparison of the extracted and parsed mean grain size data demonstrates important differences between the two. In particular, extracted measurements generally produce finer mean grain sizes, lower noise variance, and lower field variance than parsed values. Such relationships can be used to derive a regionally dependent conversion factor between the two. Our analysis of sample regions on the US continental shelf revealed considerable geographic variability in the estimated statistical parameters of field variance and decorrelation distance. Some regional relationships are evident, and overall there is a tendency for field variance to be higher where the average mean grain size is finer grained. Surprisingly, parsed and extracted noise magnitudes correlate with each other, which may indicate that some portion of the data variability that we identify as "noise" is caused by real grain size variability at very short scales. Our analyses demonstrate that by applying a bias-correction proxy, usSEABED data can be used to generate reliable interpolated maps of regional mean grain size and sediment character.

Respiration and denitrification in permeable continental shelf deposits on the South Atlantic Bight: N2:Ar and isotope pairing measurements in sediment column experiments

Alexandra Rao — 2008-05-14T19:54:56-00:00

Continental Shelf Research, Vol. 28, No. 4-5. (30 March 2008), pp. 602-613.

Mechanisms of N removal in permeable sediments were examined using sediment columns packed with southeastern US continental shelf sands. While significant N2 production was observed in oxic SAB sands, the addition of 20 [mu]M 15NO3- tracer in oxic sediment columns for periods of up to 12 days yielded a delayed production of 29N2 and 30N2 which, at the end of the incubation period, was still small relative to previously measured total N2 production rates. Possible explanations for these results include N removal via tightly coupled nitrification-denitrification in microenvironments isolated from the bulk porewater or denitrification mediated by aerobic denitrifiers. The addition of 15NO3- to porewater at levels above natural concentrations caused N assimilation and increases in sediment respiration rates in oxic columns, indicating N limitation. Delays in achieving steady-state denitrification rates following disturbances may be associated with deep penetration of O2 in advective regimes and amplified by isolation of respiration and denitrification in reactive microenvironments. Isolation of microzone denitrification, delays in achieving steady-state conditions, and the response of sediment community respiration and denitrification rates to increases in low background NO3- may interfere with the accuracy of denitrification rate measurements in sandy sediments on oligotrophic continental shelves with isotope pairing and traditional core incubation techniques. In columns with anoxic outflow, the immediate appearance of 29N2 and 30N2 following 15NO3- addition indicates that denitrification in suboxic or anoxic sands relies on external sources of NO3- rather than only on in situ nitrification, which is the main NO3- source for denitrification in oxic SAB sands.

Globally elevated titanium, tantalum, and niobium (TITAN) in ocean island basalts with high 3He/4He

Matthew Jackson — 2008-05-14T19:50:40-00:00

Geochemistry Geophysics Geosystems, Vol. 9 (17 April 2008), Q04027.

We report evidence for a global Ti, Ta, and Nb (TITAN) enriched reservoir sampled by ocean island basalts (OIBs) with high 3He/4He ratios, an isotopic signature associated with the deep mantle. Excesses of Ti (and to a lesser degree Nb and Ta) correlate remarkably well with 3He/4He in a data set of global OIBs, demonstrating that a major element signature is associated with the high 3He/4He mantle. Additionally, we find that OIBs with high 3He/4He ratios have moderately radiogenic 187Os/188Os (>0.135). The TITAN enrichment and radiogenic 187Os/188Os in high 3He/4He OIBs indicate that they are melts of a mantle domain that hosts a nonprimitive (nonchondritic) component. The observation of TITAN enrichment in the high 3He/4He mantle may be important in balancing the Earth's budget for the TITAN elements. Understanding the origin of the TITAN enrichment is important for constraining the evolution of the enigmatic high 3He/4He mantle domain.

Acoustic pressure and particle motion thresholds in six sciaenid fishes

Andrij Horodysky — 2008-05-14T19:49:55-00:00

J Exp Biol, Vol. 211, No. 9. (1 May 2008), pp. 1504-1511.

Sciaenid fishes are important models of fish sound production, but investigations into their auditory abilities are limited to acoustic pressure measurements on five species. In this study, we used auditory brainstem response (ABR) to assess the pressure and particle acceleration thresholds of six sciaenid fishes commonly found in Chesapeake Bay, eastern USA: weakfish (Cynoscion regalis), spotted seatrout (Cynoscion nebulosus), Atlantic croaker (Micropogonias undulatus), red drum (Sciaenops ocellatus), spot (Leiostomus xanthurus) and northern kingfish (Menticirrhus saxatilis). Experimental subjects were presented with pure 10 ms tone bursts in 100 Hz steps from 100 Hz to 1.2 kHz using an airborne speaker. Sound stimuli, monitored with a hydrophone and geophone, contained both pressure and particle motion components. Sound pressure and particle acceleration thresholds varied significantly among species and between frequencies; audiograms were notably flatter for acceleration than pressure at low frequencies. Thresholds of species with diverticulae projecting anteriorly from their swim bladders (weakfish, spotted seatrout, and Atlantic croaker) were typically but not significantly lower than those of species lacking such projections (red drum, spot, northern kingfish). Sciaenids were most sensitive at low frequencies that overlap the peak frequencies of their vocalizations. Auditory thresholds of these species were used to estimate idealized propagation distances of sciaenid vocalizations in coastal and estuarine environments. 10.1242/jeb.016196

Laboratory experiments on mesoscale vortices colliding with an island chain

Aya Tanabe — 2008-05-14T19:48:43-00:00

Journal of Geophysical Research, Vol. 113 (17 April 2008), C04022.

The present laboratory study investigates the behavior of a self-propagating barotropic cyclonic vortex colliding perpendicularly with aligned circular cylinders and determines the condition for a vortex to bifurcate and split into multiple vortices and/or to generate dipoles downstream of the cylinders. During the experiments, four parameters were varied: G, the gap width between the cylinders; d, the diameter of the incident vortex; Y dis , a parameter expressing the initial vortex positions; and D isl , the total length of the “middle” island. It has been observed that as long as 0.1 < G/d ≤ 0.4, the vortex fluid was funneled between two cylinders at one of the gaps and a dipole generally formed, much like water ejected from a circular nozzle generates a dipole ring. After the dipole formed, the cyclonic part of the dipole became dominant and self propagated away from the cylinders. Furthermore, in some experiments having 0.2 < D isl /d ≤ 0.5, after a weak dipole formed, the remnant of the original vortex moved zonally “south.” When the remnant of the vortex came in contact with a new cylinder, fluid peeled off the outer edge of the vortex and a so-called “streamer” went around the cylinder in a counterclockwise direction. Under the right conditions, this fluid formed a new cyclonic vortex in the wake of the cylinder, causing bifurcation of the original vortex into two vortices, as observed in previous studies. In general, independently of the configurations and Y dis , the number of cyclonic vortices downstream of the cylinders was one, either originating from the dipole or generated by the bifurcation of the original vortex. The vortex center position, radius, and circulation, before and after the interaction, were computed from its velocity field. It was found that for 0.1 < G/d ≤ 0.4, intense vortices experienced greater amplitude loss than weak vortices. The formation of both a dominant cyclone and an anticyclone (i.e., a dipole) downstream of the aligned cylinders, representing an island chain, is in agreement with recent oceanic observations of North Brazil Current (NBC) rings interacting with the Lesser Antilles in the Eastern Caribbean Sea. Since the passages of the Lesser Antilles have values of 0.07 ≤ G/d ≤ 0.3, the oceanic observations might be explained by the experimental results reported in this paper.

Modeling whale entanglement injuries: An experimental study of tissue compliance, line tension, and draw-length

Jeremy Winn — 2008-04-23T06:58:40-00:00

Marine Mammal Science, Vol. 24, No. 2. (April 2008), pp. 326-340.

Balancing bias and precision in capture-recapture estimates of abundance

Nancy Friday — 2008-04-23T06:58:41-00:00

Marine Mammal Science, Vol. 24, No. 2. (April 2008), pp. 253-275.

Capture-recapture estimates of abundance using photographic identification data are sensitive to the quality of photographs used and distinctiveness of individuals in the population. Here analyses are presented for examining the effects of photographic quality and individual animal distinctiveness scores and for objectively selecting a subset of data to use for capture-recapture analyses using humpback whale (Megaptera novaeangliae) data from a 2-year study in the North Atlantic. Photographs were evaluated for their level of quality and whales for their level of individual distinctiveness. Photographic quality scores had a 0.21 probability of changing by a single-quality level, and there were no changes by two or more levels. Individual distinctiveness scores were not independent of photographic quality scores. Estimates of abundance decreased as poor-quality photographs were removed. An appropriate balance between precision and bias in abundance estimates was achieved by removing the lowest-quality photographs and those of incompletely photographed flukes given our assumptions about the true population abundance. A simulation of the selection process implied that, if the estimates are negatively biased by heterogeneity, the increase in bias produced by decreasing the sample size is not more than 2%. Capture frequencies were independent of individual distinctiveness scores.

In situ strength measurements on natural upper-mantle minerals

Junji Yamamoto — 2008-05-14T19:43:06-00:00

Physics and Chemistry of Minerals, Vol. 35, No. 5. (22 June 2008), pp. 249-257.

Abstract Using in situ strength measurements at pressures up to 10 GPa and at room temperature, 400, 600, and 700°C, we examined rheological properties of olivine, orthopyroxene, and chromian-spinel contained in a mantle-derived xenolith. Mineral strengths were estimated using widths of X-ray diffraction peaks as a function of pressure, temperature, and time. Differential stresses of all minerals increase with increasing pressure, but they decrease with increasing temperature because of elastic strain on compression and stress relaxation during heating. During compression at room temperature, all minerals deform plastically at differential stress of 4–6 GPa. During subsequent heating, thermally induced yielding is observed in olivine at 600°C. Neither orthopyroxene nor spinel shows complete stress relaxation, but both retain some stress even at 700°C. The strength of the minerals decreases in the order of chromian-spinel ≈ orthopyroxene > olivine for these conditions. This order of strength is consistent with the residual pressure of fluid inclusions in mantle xenoliths.