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A global coupled ocean-atmosphere modeling system is applied in a transient climate simulation to study the response to global warming of Dimethylsulfide (DMS) in the ocean, the DMS flux to the atmosphere, and the resulting DMS concentrations in the atmosphere. The DMS production and consumption processes in the ocean are linked to plankton dynamics simulated in the marine biogeochemistry model HAMOCC5.1, embedded in an ocean general circulation model (MPI-OM). The atmospheric model ECHAM5 is extended by the microphysical aerosol model HAM, treating the sulfur chemistry in the atmosphere and the evolution of microphysically interacting internally and externally mixed aerosol populations. For future conditions (2000-2100) we assume greenhouse gas concentrations, aerosol and aerosol precursor emissions according to the SRES A1B scenario. We analyzed the results in terms of simulated changes between the period 1861-1890 and 2061-2090. For the global annual mean DMS sea surface concentration and the DMS flux we found a reduction by 10%. The DMS burden in the atmosphere is reduced by only 3%, owing to a longer lifetime of DMS in the atmosphere in a warmer climate (+7%). Regionally the response and the underlying mechanisms are quite inhomogeneous. The largest reduction in the DMS sea surface concentration is simulated in the Southern Ocean (-40%) caused by an increase in the summer mixed layer depth, leading to less favorable light conditions for phytoplankton growth. In the mid and low latitudes DMS sea surface concentrations are predominantly reduced due to nutrient limitation of the phytoplankton growth through higher ocean stratification and less transport of nutrients into the surface layers. Copyright 2007 by the American Geophysical Union.

The human pathogen Kaposi's sarcoma-associated herpesvirus (KSHV), the etiological agent of Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease, establishes lifelong latency upon infection. Murine gammaherpesvirus 68 (MHV68) is a well-established model for KSHV. Toll-like receptors (TLRs) play a crucial role for the innate immune response to pathogens. Although KSHV and MHV68 are detected by TLRs, studies suggest they modulate TLR4 and TLR9 signaling, respectively. In this study we show that in bone marrow-derived macrophages (BMDMs), MHV68 did not induce a detectable proinflammatory cytokine response. Furthermore, MHV68 abrogated the response to TLR2, 4, 7, and 9 agonists in BMDMs. Similarly to observations with MHV68, infection with KSHV efficiently inhibited TLR2 signaling in THP-1 monocytes. Using a KSHV ORF library, we found that K4.2, ORF21, ORF31, and RTA/ORF50 inhibited TLR2-dependent nuclear factor kappa B (NF-κB) activation in HEK293 TLR2-YFP and Flag-TLR2 transfected HEK 293T cells. Of the identified ORFs, the replication and transcription activator protein, RTA/ORF50, strongly downregulated TLR2 and TLR4 signaling by reducing TLR2 and TLR4 protein expression. Confocal microscopy revealed that TLR2 and TLR4 were no longer localized to the plasma membrane in cells expressing RTA/ORF50. In this study, we have shown that the gammaherpesviruses MHV68 and KSHV efficiently downmodulate TLR signaling in macrophages and have identified a novel function of RTA/ORF50 in modulation of the innate immune response. Importance Statement The Toll-like receptors (TLR) are an important class of pattern recognition receptors of the innate immune system. They induce a potent proinflammatory cytokine response upon detection of a variety of pathogens. In this study, we found that the gammaherpesviruses murine gammaherpesvirus 68 (MHV68) and Kaposi's sarcoma-associated herpesvirus (KSHV) efficiently inhibit the TLR-mediated innate immune response. We further identified the KSHV-encoded replication and transcription activator protein (RTA) as a novel modulator of TLR signaling. Our data suggest that the gammaherpesviruses MHV68 and KSHV prevent activation of the innate immune response by targeting TLR signaling.

Purpose Specific absorption rate is a serious problem at high field strengths, especially for sequences involving many high power radiofrequency pulses, such as turbo spin echo (TSE). GRASE (gradient and spin echo) may overcome this problem by omitting a certain number of refocusing pulses of a TSE sequence, and replacing them with segmented echo-planar imaging readouts. MethodsGRASE and TSE were compared using similar sequence parameters at a field strength of 7T. The signal-to-noise ratio (SNR) per unit time, contrast, and point spread function (PSF) were determined. High-resolution human brain images were acquired and the implementation of an inversion recovery preparation for T1 weighting was evaluated. ResultsTSE and GRASE images at 7T showed very similar SNR and contrast. The slightly worse PSF for GRASE is balanced by a significant reduction in scan time or increase in spatial coverage compared with TSE. Furthermore, implementing an additional inversion recovery preparation enables the acquisition of T1-weighted images with high SNR per unit time. ConclusionGRASE is highly suitable for structural scanning at ultra-high field strengths and is a valid alternative to the commonly used TSE sequence. Magn Reson Med 72:1291-1301, 2014.

Shelves have been estimated to account for more than one-fifth of the global marine primary production. It has been also conjectured that shelves strongly influence the oceanic absorption of anthropogenic CO2 (carbon shelf pump). Owing to their coarse resolution, currently applied global climate models are inappropriate to investigate the impact of climate change on shelves and regional models do not account for the complex interaction with the adjacent open ocean. In this study, a global ocean general circulation model and biogeochemistry model were set up with a distorted grid providing a maximal resolution for the NW European shelf and the adjacent northeast Atlantic. Using model climate projections we found that already a~moderate warming of about 2.0 K of the sea surface is linked with a reduction by ~ 30% of the biological production on the NW European shelf. If we consider the decline of anthropogenic riverine eutrophication since the 1990s, the reduction of biological production amounts is even larger. The relative decline of NW European shelf productivity is twice as strong as the decline in the open ocean (~ 15%). The underlying mechanism is a spatially well confined stratification feedback along the continental shelf break. This feedback reduces the nutrient supply from the deep Atlantic to about 50%. In turn, the reduced productivity draws down CO2 absorption in the North Sea by ~ 34% at the end of the 21st century compared to the end of the 20th century implying a strong weakening of shelf carbon pumping. Sensitivity experiments with diagnostic tracers indicate that not more than 20% of the carbon absorbed in the North Sea contributes to the long-term carbon uptake of the world ocean. The rest remains within the ocean's mixed layer where it is exposed to the atmosphere. The predicted decline in biological productivity, and decrease of phytoplankton concentration (in the North Sea by averaged 25%) due to reduced nutrient imports from the deeper Atlantic will probably affect the local fish stock negatively and therefore fisheries in the North Sea.

This paper presents an estimate of the oceanic Lorenz energy cycle derived from a simulation forced by 6-hourly fluxes obtained from NCEP–NCAR reanalysis-1. The total rate of energy generation amounts to 6.6 TW, of which 1.9 TW is generated by the time-mean winds and 2.2 TW by the time-varying winds. The dissipation of kinetic energy amounts to 4.4 TW, of which 3 TW originate from the dissipation of eddy kinetic energy. The energy exchange between reservoirs is dominated by the baroclinic pathway and the pathway that distributes the energy generated by the time-mean winds. The former converts 0.7 to 0.8 TW mean available potential energy to eddy available potential energy and finally to eddy kinetic energy, whereas the latter converts 0.5 TW mean kinetic energy to mean available potential energy.This energy cycle differs from the atmospheric one in two aspects. First, the generation of the mean kinetic and mean available potential energy is each, to a first approximation, balanced by the dissipation. The interaction of the oceanic general circulation with mesoscale eddies is hence less crucial than the corresponding interaction in the atmosphere. Second, the baroclinic pathway in the ocean is facilitated not only by the surface buoyancy flux but also by the winds through a conversion of 0.5 TW mean kinetic energy to mean available potential energy. In the atmosphere, the respective conversion is almost absent and the baroclinic energy pathway is driven solely by the differential heating.

Numerical models that combine weather forecasting and atmospheric chemistry are here referred to as chemical weather forecasting models. Eighteen operational chemical weather forecasting models on regional and continental scales in Europe are described and compared in this article. Topics discussed in this article include how weather forecasting and atmospheric chemistry models are integrated into chemical weather forecasting systems, how physical processes are incorporated into the models through parameterization schemes, how the model architecture affects the predicted variables, and how air chemistry and aerosol processes are formulated. In addition, we discuss sensitivity analysis and evaluation of the models, user operational requirements, such as model availability and documentation, and output availability and dissemination. In this manner, this article allows for the evaluation of the relative strengths and weaknesses of the various modelling systems and modelling approaches. Finally, this article highlights the most prominent gaps of knowledge for chemical weather forecasting models and suggests potential priorities for future research directions, for the following selected focus areas: emission inventories, the integration of numerical weather prediction and atmospheric chemical transport models, boundary conditions and nesting of models, data assimilation of the various chemical species, improved understanding and parameterization of physical processes, better evaluation of models against data and the construction of model ensembles. © 2012 Author(s).

Continental shelf seas are known to support a large fraction of the global primary production. Yet, they are mostly ignored or neglected in global biogeochemical models. A number of processes that control the transfer of dissolved nutrients from rivers to the open ocean remain poorly understood. This applies in particular to dissolved silica which drives the growth of diatoms that form a large part of the phytoplankton biomass and are thus an important contributor to export production of carbon. Here, the representation of the biogeochemical cycling along continents is improved by coupling a high resolution database of riverine fluxes of nutrients to the global biogeochemical ocean general circulation model HAMOCC5-OM. Focusing on silicon (Si), but including the whole suite of nutrients – carbon (C), nitrogen (N) and phosphorus (P) in various forms – inputs are implemented in the model at coastal coupling points using the COSCAT global database of 156 mega-river-ensemble catchments from Meybeck et al. (2006). The catchments connect to the ocean through coastal segments according to three sets of criteria: natural limits, continental shelf topography, and geophysical dynamics. According to the model the largest effects on nutrient concentrations occur in hot spots such as the Amazon plume, the Arctic – with high nutrient inputs in relation to its total volume, and areas that encounter the largest increase in human activity, e.g., Southern Asia.

Ocean acidification is likely to impact calcification rates in many pelagic organisms, which may in turn cause significant changes in marine ecosystem structure. We examine effects of changes in marine CaCO3 production on total alkalinity (TA) in the ocean using the global biogeochemical ocean model HAMOCC. We test a variety of future calcification scenarios because experimental studies with different organisms have revealed a wide range of calcification sensitivities to CaCO3 saturation state. The model integrations start at a preindustrial steady state in the year 1800 and run until the year 2300 forced with anthropogenic CO2 emissions. Calculated trends in TA are evaluated taking into account the natural variability in ocean carbonate chemistry, as derived from repeat hydrographic transects. We conclude that the data currently available does not allow discerning significant trends in TA due to changes in pelagic calcification caused by ocean acidification. Given different calcification scenarios, our model calculations indicate that the TA increase over time will start being detectable by the year 2040, increasing by 5-30 mu mol kg(-1) compared to the present-day values. In a scenario of extreme reductions in calcification, large TA changes relative to preindustrial conditions would have occurred at present, which we consider very unlikely. However, the time interval of reliable TA observations is too short to disregard this scenario. The largest increase in surface ocean TA is predicted for the tropical and subtropical regions. In order to monitor and quantify possible early signs of acidification effects, we suggest to specifically target those regions during future ocean chemistry surveys.

HOPE is a primitive-equation model of the global ocean circulation, but may also be used for regional studies. Prognostic variables are the three-dimensional horizontal velocity fields, the sea-surface elevation, and the thermohaline variables. The equa- tions are discretized on prescribed horizontal surfaces using Arakawa-E-type grids. Two time levels are used for the integration. A Hibler-type dynamic sea-ice model allows a prognostic calculation of sea-ice thick- ness, compactness, and velocities. The thermodynamic growth of sea ice is calculated with heat balance equations using simple bulk formulae. A snow layer is included. HOPE is in particular useful for altimetry data assimilation purposes because of the prognostic calculation of the sea-surface elevation.

The Hamburg Oceanic Carbon Cycle Circulation Model (Cycle 1)

Several multi-century and multi-millennia simulations have been performed with a complex Earth System Model (ESM) for different anthropogenic climate change scenarios in order to study the long-term evolution of sea level and the impact of ice sheet changes on the climate system. The core of the ESM is a coupled coarse-resolution Atmosphere–Ocean General Circulation Model (AOGCM). Ocean biogeochemistry, land vegetation and ice sheets are included as components of the ESM. The Greenland Ice Sheet (GrIS) decays in all simulations, while the Antarctic ice sheet contributes negatively to sea level rise, due to enhanced storage of water caused by larger snowfall rates. Freshwater flux increases from Greenland are one order of magnitude smaller than total freshwater flux increases into the North Atlantic basin (the sum of the contribution from changes in precipitation, evaporation, run-off and Greenland meltwater) and do not play an important role in changes in the strength of the North Atlantic Meridional Overturning Circulation (NAMOC). The regional climate change associated with weakening/collapse of the NAMOC drastically reduces the decay rate of the GrIS. The dynamical changes due to GrIS topography modification driven by mass balance changes act first as a negative feedback for the decay of the ice sheet, but accelerate the decay at a later stage. The increase of surface temperature due to reduced topographic heights causes a strong acceleration of the decay of the ice sheet in the long term. Other feedbacks between ice sheet and atmosphere are not important for the mass balance of the GrIS until it is reduced to 3/4 of the original size. From then, the reduction in the albedo of Greenland strongly accelerates the decay of the ice sheet.

Results are presented of export production, dissolved organic matter (DOM) and dissolved oxygen simulated by 12 global ocean models participating in the second phase of the Ocean Carbon-cycle Model Intercomparison Project. A common, simple biogeochemical model is utilized in different coarse-resolution ocean circulation models. The model mean (+/- 1 sigma) downward flux of organic matter across 75 m depth is 17 +/- 6 Pg C yr(-1). Model means of globally averaged particle export, the fraction of total export in dissolved form, surface semilabile dissolved organic carbon (DOC), and seasonal net outgassing (SNO) of oxygen are in good agreement with observation-based estimates, but particle export and surface DOC are too high in the tropics. There is a high sensitivity of the results to circulation, as evidenced by (1) the correlation of surface DOC and export with circulation metrics, including chlorofluorocarbon inventory and deep-ocean radiocarbon, (2) very large intermodel differences in Southern Ocean export, and (3) greater export production, fraction of export as DOM, and SNO in models with explicit mixed layer physics. However, deep-ocean oxygen, which varies widely among the models, is poorly correlated with other model indices. Cross-model means of several biogeochemical metrics show better agreement with observation-based estimates when restricted to those models that best simulate deep-ocean radiocarbon. Overall, the results emphasize the importance of physical processes in marine biogeochemical modeling and suggest that the development of circulation models can be accelerated by evaluating them with marine biogeochemical metrics. [References: 112]

We implemented a process-based DMS module into the global carbon cycle ocean model (HAMOCC5) which includes a simple module for plankton dynamics and investigated the regional and seasonal variations of the marine sulfur cycle. The turnover rates within the DMS cycle are only poorly known. Therefore we developed, on the basis of a global DMS data set, an optimization routine for the free parameters controlling DMS production and removal. The resulting seasonal and regional distributions of DMS concentration are fully consistent with the underlying hydrodynamical and biogeochemical processes. We investigated a series of DMS model approaches with various complexities. The distinction between different DMS producing phytoplankton species and the consideration of the regionally and seasonally varying bacterial activity on converting dDMSP to DMS and on DMS consumption appears to have a crucial effect on the quality of the results in the given model conception.

The Arctic polar vortex exhibited widespread regions of low temperatures during the winter of 2005, resulting in significant ozone depletion by chlorine and bromine species. We show that chemical loss of column ozone (ΔO3) and the volume of Arctic vortex air cold enough to support the existence of polar stratospheric clouds (VPSC) both exceed levels found for any other Arctic winter during the past 40 years. Cold conditions and ozone loss in the lowermost Arctic stratosphere (e.g., between potential temperatures of 360 to 400 K) were particularly unusual compared to previous years. Measurements indicate ΔO3 = 121 ± 20 DU and that ΔO3 versus VPSC lies along an extension of the compact, near linear relation observed for previous Arctic winters. The maximum value of VPSC during five to ten year intervals exhibits a steady, monotonic increase over the past four decades, indicating that the coldest Arctic winters have become significantly colder, and hence are more conducive to ozone depletion by anthropogenic halogens. Copyright 2006 by the American Geophysical Union.

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