The Drosophila chk2 gene loki is essential for embryonic DNA double-strand-break checkpoints induced in S phase or G2

Cell cycle checkpoints are signal transduction pathways that control the order and timing of cell cycle transitions, ensuring that critical events are completed before the occurrence of the next cell cycle transition. The Chk2 family of kinases is known to play a central role in mediating the cellular responses to DNA damage or DNA replication blocks in various organisms. Here we show through a phylogenetic study that the Drosophila melanogaster serine/threonine kinase Loki is the homolog of the yeast Mek1p, Rad53p, Dun1p, and Cds1 proteins as well as the human Chk2. Functional analyses allowed us to conclude that, in flies, chk2 is involved in monitoring double-strand breaks (DSBs) caused by irradiation during S and G2 phases. In this process it plays an essential role in inducing a cell cycle arrest in embryonic cells. Our results also show that, in contrast to C. elegans chk2, Drosophila chk2 is not essential for normal meiosis and recombination, and it also appears to be dispensable for the MMS-induced DNA damage checkpoint and the HU-induced DNA replication checkpoint during larval development. In addition, Drosophila chk2 does not act at the same cell cycle phases as its yeast homologs, but seems rather to be involved in a pathway similar to the mammalian one, which involves signaling through the ATM/Chk2 pathway in response to genotoxic insults. As mutations in human chk2 were linked to several cancers, these similarities point to the usefulness of the Drosophila model system.

High-resolution in situ oxygen microprofiles, porewater and solid phase geochemistry from the Crimean shelf (Black Sea) from Maria S. Merian cruise MSM15/1

The outer western Crimean shelf of the Black Sea is a natural laboratory to investigate effects of stable oxic versus varying hypoxic conditions on seafloor biogeochemical processes and benthic community structure. Bottom-water oxygen concentrations ranged from normoxic (175 µmol O2/L) and hypoxic (< 63 µmol O2/L) or even anoxic/sulfidic conditions within a few kilometers' distance. Variations in oxygen concentrations between 160 and 10 µmol/L even occurred within hours close to the chemocline at 134 m water depth. Total oxygen uptake, including diffusive as well as fauna-mediated oxygen consumption, decreased from 15 mmol/m**2/d on average in the oxic zone, to 7 mmol/m**2/d on average in the hypoxic zone, correlating with changes in macrobenthos composition. Benthic diffusive oxygen uptake rates, comprising respiration of microorganisms and small meiofauna, were similar in oxic and hypoxic zones (on average 4.5 mmol/m**2/d), but declined to 1.3 mmol/m**2/d in bottom waters with oxygen concentrations below 20 µmol/L. Measurements and modeling of porewater profiles indicated that reoxidation of reduced compounds played only a minor role in diffusive oxygen uptake under the different oxygen conditions, leaving the major fraction to aerobic degradation of organic carbon. Remineralization efficiency decreased from nearly 100 % in the oxic zone, to 50 % in the oxic-hypoxic zone, to 10 % in the hypoxic-anoxic zone. Overall, the faunal remineralization rate was more important, but also more influenced by fluctuating oxygen concentrations, than microbial and geochemical oxidation processes.

Total nitrogen from solid phase in the Jena Experiment (Main Experiment up to 30cm depth, year 2008)

This data set contains measurements of total nitrogen from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling was performed in April 2008 to a depth of 30 cm. Three independent samples per plot were taken using a split tube sampler with an inner diameter of 4.8 cm (Eijkelkamp Agrisearch Equipment, Giesbeek, the Netherlands). Soil samples were segmented to a depth resolution of 5 cm in the field, giving six depth subsamples per core, and made into composite samples per depth. Sampling locations were less than 30 cm apart from sampling locations in other years. Samples were dried at 40°C. All soil samples were passed through a sieve with a mesh size of 2 mm. Because of much higher proportions of roots in the soil, the samples were further sieved to 1 mm according to common root removal methods. No additional mineral particles were removed by this procedure. Total nitrogen concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany).

Total nitrogen from solid phase in the Jena Experiment (Block 2 Main Experiment up to 100cm depth, year 2002)

This data set contains measurements of total nitrogen from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling to a depth of 1m was performed before sowing in April 2002. Three independent samples per plot were taken of all plots in block 2 using a motor-driven soil column cylinder (Cobra, Eijkelkamp, 8.3 cm in diameter). Soil samples were dried at 40°C and segmented to a depth resolution of 5 cm giving 20 depth subsamples per core. All samples were analyzed independently. All soil samples were passed through a sieve with a mesh size of 2 mm. Rarely present visible plant remains were removed using tweezers. Total nitrogen concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany).

Total nitrogen from solid phase in the Jena Experiment (Main Experiment up to 30cm depth, year 2004)

This data set contains measurements of total nitrogen from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling was performed in April 2004 to a depth of 30 cm. Three independent samples per plot were taken using a split tube sampler with an inner diameter of 4.8 cm (Eijkelkamp Agrisearch Equipment, Giesbeek, the Netherlands). Soil samples were segmented to a depth resolution of 5 cm in the field, giving six depth subsamples per core, and made into composite samples per depth. Sampling locations were less than 30 cm apart from sampling locations in other years. Samples were dried at 40°C. All soil samples were passed through a sieve with a mesh size of 2 mm. Because of much higher proportions of roots in the soil, the samples were further sieved to 1 mm according to common root removal methods. No additional mineral particles were removed by this procedure. Total nitrogen concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany).

Elemental and stable isotopic composition of some metalliferous and pelagic sediments at DSDP Leg 70 Holes

Nontronite, the main metalliferous phase of the Galapagos mounds, occurs at subsurface depths of about 2 to 20 meters; Mn-oxide material is limited to the upper 2 meters of the mounds. The nontronite forms intervals of up to a few meters' thickness, consisting essentially of 100% nontronite granules, which alternate with intervals of normal pelagic sediment. Electron microprobe analyses of nontronite granules from different core samples indicate that: (1) there is little difference in major element composition between nontronites from varying locations within the mounds, with adjacent granules from a given sample having very similar compositions; (2) individual granules show little internal variation in composition. This indicates that the granules are composed of a single mineral of essentially constant composition, consistent with relatively uniform conditions of Eh and composition during nontronite formation. Mn-oxide crusts have very low Fe contents, a feature characteristic of rapidly deposited Mn-oxide crusts formed under hydrothermal influences. The rare-earth element (REE) abundances of the nontronites are generally extremely low, totalling less than several ppm. Two samples have the negatively Ce anomaly typical of authigenic precipitates formed relatively rapidly from seawater. A Mn-oxide crust sample has low REE contents, typical of Mn-oxide crusts formed under hydrothermal influences, but no negative Ce anomaly. A sample of unusual Mn-Fe-oxide mud has relatively high REE concentrations and a seawater-type pattern; both of these features are also found for metalliferous sediments from the East Pacific Rise. The oxygen and hydrogen isotopic composition of the nontronites define a restricted field within a d18O-dD plot. In manganiferous sediments, d18O and dD appear to decrease with increase in the Mn-oxide content of the sediment. From the d18O values of the nontronites, formation temperatures in the range of about 20-30°C have been estimated. By comparison, temperatures of up to 11.5 °C at a 9-meter depth have been directly measured within the mounds (Corliss et al., 1979), and heat-flow data suggest present basement/sediment interface temperatures of 15-25°C. In a plot of Fe + Mn vs. d18O, the Mn-oxide crust and Mn-Fe-ooze plot near the tie-lines for authigenic Mn nodules and silicate phases, implying that they have formed in isotopic equilibrium with seawater at or close to bottom-water temperatures.

Age model and elemental data of DSDP Holes 48-401 and 80-549

A growing body of geologic evidence suggests that emplacement of the North Atlantic Igneous Province (NAIP) played a major role in global warming during the early Paleogene as well as in the transient Paleocene-Eocene thermal maximum (PETM) event. A ~5 million year record of major and trace element abundances spanning 56 to 51 Ma at Deep Sea Drilling Project Sites 401 and 549 confirms that the majority of NAIP volcanism occurred as subaerial flows. Thus the trace element records provide constraints on the nature and scope of the environmental impact of the NAIP during the late Paleocene-early Eocene interval. Subaerial volcanism would have injected mantle CO2 directly into the atmosphere, resulting in a more immediate increase in atmospheric greenhouse gas abundances than CO2 input through submarine volcanism. The lack of significant hydrothermalism contradicts recently proposed mechanisms for thermally destabilizing methane hydrate reservoirs during the PETM. Any connection between NAIP volcanism and PETM warming had to occur through the atmosphere.

Pore water (SO4, CH4, alkalinity, HS-, Ca, Sr, Mg, Ba) and solid phase (Ca, Sr, Mg, Ba) data measured in pockmark sediments of the Northern Congo Fan

This study focuses on the vertical distribution of authigenic carbonates (aragonite and high Mg-calcite) in the form of finely disseminated precipitates as well as massive carbonate concretions present in and above gas hydrate bearing sediments of the Northern Congo Fan. Analyses of Ca, Mg, Sr and Ba in pore water, bulk sediments and authigenic carbonates were carried out on gravity cores taken from three pockmark structures (Hydrate Hole, Black Hole and Worm Hole). In addition, a background core was retrieved from an area not influenced by fluid seepage. Pore water Sr/Ca and Mg/Ca ratios are used to reveal the current depths of carbonate formation as well as the mineralogy of the authigenic precipitates. The Sr/Ca and Mg/Ca ratios of bulk sediments and massive carbonate concretions were applied to infer the presence and depth distribution of authigenic aragonite and high Mg-calcite, based on the approach presented by Bayon et al. [Bayon et al. (2007). Sr/Ca and Mg/Ca ratios in Niger Delta sediments: Implications for authigenic carbonate genesis in cold seep environments. Marine Geology 241(1-4), 93-109, doi:10.1016/j.margeo.2007.03.007]. We show that the approach developed by Bayon et al. (2007) for sediments of cold seeps of the Niger Delta is also suitable to identify the mineralogy of authigenic carbonates in pockmark sediments of the Congo Deep-Sea Fan. We expand this approach by combining interstitial with solid phase Sr/Ca and Mg/Ca ratios, which demonstrate that high Mg-calcite is the predominant authigenic carbonate that currently forms at the sulfate/methane reaction zone (SMRZ). This is the first study which investigates both solid phase and pore water signatures typical for either aragonite or high Mg-calcite precipitation for the same sediment cores and thus is able to identify active and fossil carbonate precipitation events. At all investigated pockmark sites fossil horizons of the SMRZ were deduced from high Mg-calcite located above and below the current depths of the SMRZ. Additionally, aragonite enrichments typical for high seepage rates were detected close to the sediment surface at these sites. However, active precipitation of aragonite as indicated by pore water characteristics only occurs at the Black Hole site. Dissolved and solid phase Ba concentrations were used to estimate the time the SMRZ was fixed at the current depths of the diagenetic barite fronts. The combined pore water and solid phase elemental ratios (Mg/Ca, Sr/Ca) and Ba concentrations allow the reconstruction of past changes in methane seepage at the investigated pockmark sites. At the Hydrate Hole and Worm Hole sites the time of high methane seepage was estimated to have ceased at least 600 yr BP. In contrast, a more recent change from a high flux to a more dormant stage must have occurred at the Black Hole site as evidenced by active aragonite precipitation at the sediment surface and a lack of diagenetic Ba enrichments.

Pore water and solid phase sulfur, carbon and iron data from samples collected in the Argentine Basin during expedition M78

Sulfur phases in the Argentine Basin.

Elemental and isotopic compositions of metalliferous and pelagic sediments from the Galapagos mounds area, data of DSDP Leg 70

Nontronite, the main metalliferous phase of the Galapagos mounds, occurs at a subsurface depth of ~2-20 m; Mn-oxide material is limited to the upper 2 m of these mounds. The nontronite forms intervals of up to a few metres thickness, consisting essentially of 100% nontronite granules, which alternate with intervals of normal pelagic sediment. The metalliferous phases represent essentially authigenic precipitates, apparently formed in the presence of upwelling basement-derived hydrothermal solutions which dissolved pre-existent pelagic sediment. Electron microprobe analyses of nontronite granules from different core samples indicate that: (1) there is little difference in major-element composition between nontronitic material from varying locations within the mounds; and (2) adjacent granules from a given sample have very similar compositions and are internally homogeneous. This indicates that the granules are composed of a single mineral of essentially constant composition, consistent with relatively uniform conditions of solution Eh and composition during nontronite formation. The Pb-isotopic composition of the nontronite and Mn-oxide sediments indicates that they were formed from solutions which contained variable proportions of basaltic Pb, introduced into pore waters by basement-derived solutions, and of normal-seawater Pb. However, the Sr-isotopic composition of these sediments is essentially indistinguishable from the value for modern seawater. On the basis of 18O/16O ratios, formation temperatures of ~20-30°C have been estimated for the nontronites. By comparison, temperatures of up to 11.5°C at 9 m depth have been directly measured within the mounds and heat flow data suggest present basement-sediment interface temperatures of 15-25°C.