Global Homogeneous Response Units

The concept of homogenous response units (HRU) was designed as a general concept for the delineation of basic spatial units. Only those characteristics of landscape, which are relatively stable over time (even under climate change) and largely unsusceptible to anthropogenic influence, were selected. The HRU can be seen as a basic spatial framework for the implementation of climate change and land management alternative scenarios into global modeling and therefore is a basic input for delineation of landscape units. HRUs are defined based on classifications of altitude (five classes: 1 (0 - 300m), 2 (300 - 600m), 3 (600 - 1100m), 4 (1100 - 2500m), 5 (> 2500m)), slope (seven classes(degrees): 1 (0 - 3), 2 (3 - 6), 3 (6 - 10), 4 (10 - 15), 5 (15 - 30), 6 (30 - 50), 7 (> 50)) and soil composition (five classes: 1 (sandy), 2 (loamy), 3 (clay), 4 (stony), 5 (peat)). e.g. HRU111 refers to Altitude class 1: 0-300m; Slope class 1: 0-3 degrees; and Soil class 1: sandy. Areas of non-soil are assigned 88. HRUs have a spatial resolution of approximately 10 km**2.

Turbulence measurements performed in the North Atlantic during the James Cook cruise JC087, March 2013

During the cruise the turbulence probe MSS050 was used for microstructure measurements. The profiler is produced by Sea and Sun Technology GmbH in co-operation with ISW Wassermesstechnik. The probe was equipped with 2 velocity microstructure shear sensors, a microstructure temperature sensor, standard CTD sensors for precision measurements, a vibration control sensor, a two component tilt sensor, a fluorescence sensor and surface detection sensor (SD) to indicate the water surface hit at rising measurements. The sampling rate for all sensors is 1024 samples per second, the resolution 16 bit. During the MSS measurements, the ship was moving with speed approx. 0.5-1.0 knots with respect to the water against the wind. In order to take into account the intermittent nature of marine turbulence, repeated MSS measurements were carried out in bursts of typically 10 profiles per station. The measurement interval was approximately 7 (10) min for a profile to 140 (200) dbar. During JC87 cruise 8 series of turbulence measurements were conducted. Fluorescence data was obtained on the 5 of them.

Water chemistry and iron speciation in samples taken during SWEDARP 97/98 campaign with S.A. Agulhas to the Southern Ocean

The distribution and speciation of iron was determined along a transect in the eastern Atlantic sector (6°E) of the Southern Ocean during a collaborative Scandinavian/South African Antarctic cruise conducted in late austral summer (December 1997/January 1998). Elevated concentrations of dissolved iron (>0.4 nM) were found at 60°S in the vicinity of the Spring Ice Edge (SIE) in tandem with a phytoplankton bloom, chiefly dominated by Phaeocystis sp. This bloom had developed rapidly after the loss of the seasonal sea ice cover. The iron that fuelled this bloom was mostly likely derived from sea ice melt. In the Winter Ice Edge (WIE), around 55°S, dissolved iron concentrations were low (<0.2 nM) and corresponded to lower biological productivity, biomass. In the Antarctic Polar Front, at approximately 50°S, a vertical profile of dissolved iron showed low concentrations (<0.2 nM); however, a surface survey showed higher concentrations (1-3 nM), and considerable patchiness in this dynamic frontal region. The chemical speciation of iron was dominated by organic complexation throughout the study region. Organic iron-complexing ligands ([L]) ranged from 0.9 to 3.0 nM Fe equivalents, with complex stability log K'(FeL) = 21.4-23.5. Estimated concentrations of inorganic iron (Fe') ranged from 0.03 to 0.79 pM, with the highest values found in the Phaeocystis bloom in the SIE. A vertical profile of iron-complexing ligands in the WIE showed a maximum consistent with a biological source for ligand production and near surface minimum possibly consistent with loss via photodecomposition. This work further confirms the role iron that has in the Southern Ocean in limiting primary productivity.

Sedimentary and subsidence history of ODP Sites 135-840 and 135-841

Sedimentary sections recovered from the Tonga platform and forearc during Ocean Drilling Program Leg 135 provide a record of the sedimentary evolution of the active margin of the Indo-Australian Plate from late Eocene time to the Present. Facies analyses of the sediments, coupled with interpretations of downhole Formation MicroScanner logs, allow the complete sedimentary and subsidence history of each site to be reconstructed. After taking into account the water depths in which the sediments were deposited and their subsequent compaction, the forearc region of the Tofua Arc (Site 841) can be seen to have experienced an initial period of tectonic subsidence dating from 35.5 Ma. Subsidence has probably been gradual since that time, with possible phases of accelerated subsidence, starting at 16.2 and 10.0 Ma. The Tonga Platform (Site 840) records only the last 7.0 Ma of arc evolution. However, the increased accuracy of paleowater depth determinations possible with shallow-water platform sediments allows the resolution of a distinct increase in subsidence rates at 5.30 Ma. Thus, sedimentology and subsidence analyses show the existence of at least two, and possibly four, separate subsidence events in the forearc region. Subsidence dating from 35.5 Ma is linked to rifting of the South Fiji Basin. Any subsidence dating from 16.2 Ma at Site 841 does not correlate with another known tectonic event and is perhaps linked to localized extensional faulting related to slab roll back during steady-state subduction. Subsidence from 10.0 Ma coincides with the breakup of the early Tertiary Vitiaz Arc because of the subduction polarity reversal in the New Hebrides and the subsequent readjustment of the plate boundary geometry. More recently, rapid subsidence and deposition of a upward-fining cycle from 5.30 Ma to the Present at Site 840 is thought to relate to rifting of the Lau Basin. Sedimentation is principally controlled by tectonic activity, with variations in eustatic sea level playing a significant, but subordinate role. Subduction of the Louisville Seamount Chain seems to have disrupted the forearc region locally, although it had only a modest effect on the subsidence history and sedimentation of the Tonga Platform as a whole.

(Table 1) Platinum group element abundanves in ODP Leg 135 samples

Ocean Drilling Program Leg 135 backarc basin lavas are characterized by anomalously high Au contents (1.0-11.4 ppb) and strongly fractionated relative platinum group element (PGE) abundances (Pd/Ir ratio, approximately 100). The Rh and Ir contents are very low, ranging from below detection (approximately 0.02 ppb) to 0.08 ppb. The Pd and Pt contents range from <0.3 to 4 ppb. Rh, Pd, and Pt values are consistently and significantly higher in Site 836 and 839 samples relative to those from Sites 834 and 835. Major, trace, and rare earth element (REE) data suggest Sites 836 and 839 have a more pronounced arc signature than Sites 834 and 835. No correlation exists between noble metal abundance and indices of alteration or fractionation (e.g., loss on ignition (LOI), Mg#, and Cr or Ni contents), suggesting that measured values and ratios are primary and reflect characteristics of the mantle source. The evaluation of Leg 135 noble metal data with respect to potential mantle-source components is hindered by the lack of data on magmas derived from such sources. However, analyses of the limited available data for the different magma types suggest that the characteristic enrichment of Leg 135 lavas in Au, relative to Pd and Cu, cannot be derived solely from simple MORB-type or ocean-island-type mantle, or mantle depleted by a previous melt extraction event. The Au-enriched signature of the Lau basin lavas could, however, be produced through the addition of a sedimentary component from the downgoing slab. Separation of Au from the PGE occurs within oceanic hydrothermal systems and gold values of the resultant precipitates are 2-3 orders of magnitude higher than other oceanic crustal components. Even small additions of this component from the downgoing oceanic crust to a supra-subduction zone mantle melt could account for the high mean Au/Pd ratios of the Leg 135 samples (Sites 834 and 835, Au/Pd = 5.04; Sites 836 and 839, Au/Pd = 2.26).

Age determination and clay content of sediment core GeoB5804-4

Paleosalinity and terrigenous sediment input changes reconstructed on two sediment cores from the northernmost Red Sea were used to infer hydrological changes at the southern margin of the Mediterranean climate zone during the Holocene. Between approximately 9.25 and 7.25 thousand years ago, about 3 per mil reduced surface water salinities and enhanced fluvial sediment input suggest substantially higher rainfall and freshwater runoff, which thereafter decreased to modern values. The northern Red Sea humid interval is best explained by enhancement and southward extension of rainfall from Mediterranean sources, possibly involving strengthened early-Holocene Arctic Oscillation patterns and a regional monsoon-type circulation induced by increased land-sea temperature contrasts. We conclude that Afro-Asian monsoonal rains did not cross the subtropical desert zone during the early to mid-Holocene.

Sedimentary cycles on the Exmouth Plateau

Sedimentary cycles are observed in the nearly complete Lower Cretaceous to Eocene pelagic carbonates at Site 762 on the Exmouth Plateau off northwest Australia. The high-frequency cycles of variable clay and foraminifers in nannofossil chalk appear as color cycles repeating on a scale of centimeters to meters in thickness. Measured cycle thickness indicate that the dominant cycles appear to be related to the precession and obliquity periods. To evaluate the high-frequency variance observed on the gamma-ray curve, spectral analysis of the log was performed on two intervals: 260 to 365 mbsf in the Cenozoic, and 555 to 685 mbsf in the Mesozoic. Average Cenozoic sedimentation rates of 10.5 m/m.y. are high enough to show that variance is present in the full suite of eccentricity bands (413-123-95 k.y.). Spectral analysis of the Mesozoic section failed to produce dominant peaks that could be correlated to predicted orbital periods. The bioturbation observed in the cores in this interval may be responsible for diluting the signal and producing high-frequency noise, which is manifested in the spectra as low, broad amplitude peaks. Orbital forcing may be affecting sedimentation on the Exmouth Plateau by influencing cycles of increased carbonate production or dissolution. Alternatively, clay abundance cycles may be related to eolian deposition during cycles of increased aridity in western Australia. Four low-frequency events were also identified at Site 762 from the core and log data. The duration of these events is approximately 13 m.y., and the conformable boundaries of these sedimentary cycles correlate with observed nondepositional surfaces in other wells in western Australia. The causal mechanism for the onset of these events may be eustatic, but alternatively may be regional tectonism with associated circulation pattern changes.

Trace element contents in zircons from oceanic crust

We present newly acquired trace element compositions for more than 300 zircon grains in 36 gabbros formed at the slow-spreading Mid-Atlantic and Southwest Indian Ridges. Rare earth element patterns for zircon from modern oceanic crust completely overlap with those for zircon crystallized in continental granitoids. However, plots of U versus Yb and U/Yb versus Hf or Y discriminate zircons crystallized in oceanic crust from continental zircon, and provide a relatively robust method for distinguishing zircons from these environments. Approximately 80% of the modern ocean crust zircons are distinct from the field defined by more than 1700 continental zircons from Archean and Phanerozoic samples. These discrimination diagrams provide a new tool for fingerprinting ocean crust zircons derived from reservoirs like that of modern mid-ocean ridge basalt (MORB) in both modern and ancient detrital zircon populations. Hadean detrital zircons previously reported from the Acasta Gneiss, Canada, and the Narryer Gneiss terrane, Western Australia, plot in the continental granitoid field, supporting hypotheses that at least some Hadean detrital zircons crystallized in continental crust forming magmas and not from a reservoir like modern MORB.

Gridded climate data from 5 Global Climate Models (GCM) of the Last Glacial Maximum (LGM) downscaled to 30 arc seconds for Europe, with links to NetCDF files

Studies on the impact of historical, current and future global change require very high-resolution climate data (less or equal 1km) as a basis for modelled responses, meaning that data from digital climate models generally require substantial rescaling. Another shortcoming of available datasets on past climate is that the effects of sea level rise and fall are not considered. Without such information, the study of glacial refugia or early Holocene plant and animal migration are incomplete if not impossible. Sea level at the last glacial maximum (LGM) was approximately 125m lower, creating substantial additional terrestrial area for which no current baseline data exist. Here, we introduce the development of a novel, gridded climate dataset for LGM that is both very high resolution (1km) and extends to the LGM sea and land mask. We developed two methods to extend current terrestrial precipitation and temperature data to areas between the current and LGM coastlines. The absolute interpolation error is less than 1°C and 0.5 °C for 98.9% and 87.8% of all pixels for the first two 1 arc degree distance zones. We use the change factor method with these newly assembled baseline data to downscale five global circulation models of LGM climate to a resolution of 1km for Europe. As additional variables we calculate 19 'bioclimatic' variables, which are often used in climate change impact studies on biological diversity. The new LGM climate maps are well suited for analysing refugia and migration during Holocene warming following the LGM.

Low-pressure melting relations of a basalt from ODP Hole 127-797C

One-atmosphere melting experiments, controlled to approximately the fayalite-magnetite-quartz oxygen buffer, performed on a basalt from Hole 797C crystallized olivine and plagioclase nearly simultaneously from about 1235°C and augite from about 1175°C. The liquid compositions indicate systematic trends of increasing FeO and TiO2 and decreasing Al2O3 with decreasing MgO. Experimental olivine compositions vary from Fo90 to Fo78, plagioclase from An79 to An67, and augite from En49 to En46. The KD value for the Fe2+ and Mg distribution between olivine and liquid is 0.31. The KD value for the distribution of Fetotal and Mg between augite and liquid averages 0.24. These KD values suggest experimental equilibrium. The KD values for Na and Ca distribution between plagioclase and liquid range between 0.55 and 0.99 and are dependent on crystallization temperature. Projected on pseudoternary basaltic phase diagrams, the liquid line of descent moves toward increasing quartz normative compositions, revealing a typical tholeiitic crystallization trend with marked Fe and Ti enrichments. Such enrichments are a reflection of the dominance of plagioclase in the crystallizing assemblage. The experimental results can explain the marked Fe- and Ti-enrichment trends observed for the sills of the lower part of Hole 797C, but have no direct bearing on the origin of the relatively evolved high-Al basalts of Hole 794C.

Nitrogen fuelling of the pelagic food web of the Tropical Atlantic

We estimated the relative contribution of atmospheric Nitrogen (N) input (wet and dry deposition and N fixation) to the epipelagic food web by measuring N isotopes of different functional groups of epipelagic zooplankton along 23°W (17°N-4°S) and 18°N (20-24°W) in the Eastern Tropical Atlantic. Results were related to water column observations of nutrient distribution and vertical diffusive flux as well as colony abundance of Trichodesmium obtained with an Underwater Vision Profiler (UVP5). The thickness and depth of the nitracline and phosphocline proved to be significant predictors of zooplankton stable N isotope values. Atmospheric N input was highest (61% of total N) in the strongly stratified and oligotrophic region between 3 and 7°N, which featured very high depth-integrated Trichodesmium abundance (up to 9.4×104 colonies m-2), strong thermohaline stratification and low zooplankton delta15N (~2 per mil). Relative atmospheric N input was lowest south of the equatorial upwelling between 3 and 5°S (27%). Values in the Guinea Dome region and north of Cape Verde ranged between 45 and 50%, respectively. The microstructure-derived estimate of the vertical diffusive N flux in the equatorial region was about one order of magnitude higher than in any other area (approximately 8 mmol m-2 d 1). At the same time, this region received considerable atmospheric N input (35% of total). In general, zooplankton delta15N and Trichodesmium abundance were closely correlated, indicating that N fixation is the major source of atmospheric N input. Although Trichodesmium is not the only N fixing organism, its abundance can be used with high confidence to estimate the relative atmospheric N input in the tropical Atlantic (r2 = 0.95). Estimates of absolute N fixation rates are two- to tenfold higher than incubation-derived rates reported for the same regions. Our approach integrates over large spatial and temporal scales and also quantifies fixed N released as dissolved inorganic and organic N. In a global analysis, it may thus help to close the gap in oceanic N budgets.

Crystal structure of the HLA-Cw3 allotype-specific killer cell inhibitory receptor KIR2DL2

Killer cell inhibitory receptors (KIR) protect class I HLAs expressing target cells from natural killer (NK) cell-mediated lysis. To understand the molecular basis of this receptor-ligand recognition, we have crystallized the extracellular ligand-binding domains of KIR2DL2, a member of the Ig superfamily receptors that recognize HLA-Cw1, 3, 7, and 8 allotypes. The structure was determined in two different crystal forms, an orthorhombic P212121 and a trigonal P3221 space group, to resolutions of 3.0 and 2.9 Å, respectively. The overall fold of this structure, like KIR2DL1, exhibits K-type Ig topology with cis-proline residues in both domains that define β-strand switching, which sets KIR apart from the C2-type hematopoietic growth hormone receptor fold. The hinge angle of KIR2DL2 is approximately 80°, 14° larger than that observed in KIR2DL1 despite the existence of conserved hydrophobic residues near the hinge region. There is also a 5° difference in the observed hinge angles in two crystal forms of 2DL2, suggesting that the interdomain hinge angle is not fixed. The putative ligand-binding site is formed by residues from several variable loops with charge distribution apparently complementary to that of HLA-C. The packing of the receptors in the orthorhombic crystal form offers an intriguing model for receptor aggregation on the cell surface.

Cloning and characterization of a plastidal and a mitochondrial isoform of tobacco protoporphyrinogen IX oxidase

Protoporphyrinogen IX oxidase is the last enzyme in the common pathway of heme and chlorophyll synthesis and provides precursor for the mitochondrial and plastidic heme synthesis and the predominant chlorophyll synthesis in plastids. We cloned two different, full-length tobacco cDNA sequences by complementation of the protoporphyrin-IX-accumulating Escherichia coli hemG mutant from heme auxotrophy. The two sequences show similarity to the recently published Arabidopsis PPOX, Bacillus subtilis hemY, and to mammalian sequences encoding protoporphyrinogen IX oxidase. One cDNA sequence encodes a 548-amino acid residues protein with a putative transit sequence of 50 amino acid residues, and the second cDNA encodes a protein of 504 amino acid residues. Both deduced protein sequences share 27.2% identical amino acid residues. The first in vitro translated protoporphyrinogen IX oxidase could be translocated to plastids, and the approximately 53-kDa mature protein was detected in stroma and membrane fraction. The second enzyme was targeted to mitochondria without any detectable reduction in size. Localization of both enzymes in subcellular fractions was immunologically confirmed. Steady-state RNA analysis indicates an almost synchronous expression of both genes during tobacco plant development, greening of young seedlings, and diurnal and circadian growth. The mature plastidal and the mitochondrial isoenzyme were overexpressed in E. coli. Bacterial extracts containing the recombinant mitochondrial enzyme exhibit high protoporphyrinogen IX oxidase activity relative to control strains, whereas the plastidal enzyme could only be expressed as an inactive peptide. The data presented confirm a compartmentalized pathway of tetrapyrrole synthesis with protoporphyrinogen IX oxidase in plastids and mitochondria.

Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray

Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5′ end- dependent scanning to initiate translation, picornaviral, hepatitis C viral, and a few cellular RNAs have been shown to be translated by internal ribosome entry, a mechanism that can operate in the presence of low levels of functional eIF4F. To identify cellular mRNAs that can be translated when eIF4F is depleted or in low abundance and that, therefore, may contain internal ribosome entry sites, mRNAs that remained associated with polysomes were isolated from human cells after infection with poliovirus and were identified by using a cDNA microarray. Approximately 200 of the 7000 mRNAs analyzed remained associated with polysomes under these conditions. Among the gene products encoded by these polysome-associated mRNAs were immediate-early transcription factors, kinases, and phosphatases of the mitogen-activated protein kinase pathways and several protooncogenes, including c-myc and Pim-1. In addition, the mRNA encoding Cyr61, a secreted factor that can promote angiogenesis and tumor growth, was selectively mobilized into polysomes when eIF4F concentrations were reduced, although its overall abundance changed only slightly. Subsequent tests confirmed the presence of internal ribosome entry sites in the 5′ noncoding regions of both Cyr61 and Pim-1 mRNAs. Overall, this study suggests that diverse mRNAs whose gene products have been implicated in a variety of stress responses, including inflammation, angiogenesis, and the response to serum, can use translational initiation mechanisms that require little or no intact cap binding protein complex eIF4F.

Numbers and Organization of RNA Polymerases, Nascent Transcripts, and Transcription Units in HeLa Nuclei

Using HeLa cells, we have developed methods to determine 1) the number of RNA polymerases that are active at any moment, 2) the number of transcription sites, and 3) the number of polymerases associated with one transcription unit. To count engaged polymerases, cells were encapsulated in agarose, permeabilized, treated with ribonuclease, and the now-truncated transcripts extended in [32P]uridine triphosphate; then, the number of growing transcripts was calculated from the total number of nucleotides incorporated and the average increment in length of the transcripts. Approximately 15,000 transcripts were elongated by polymerase I, and ∼75,000 were elongated by polymerases II and III. Transcription sites were detected after the cells were grown in bromouridine for <2.5 min, after which the resulting bromo-RNA was labeled with gold particles; electron microscopy showed that most extranucleolar transcripts were concentrated in ∼2400 sites with diameters of ∼80 nm. The number of polymerases associated with a transcription unit was counted after templates were spread over a large area; most extranucleolar units were associated with one elongating complex. These results suggest that many templates are attached in a “cloud” of loops around a site; each site, or transcription “factory,” would contain ∼30 active polymerases and associated transcripts.