Percentage of cultured cell-populations that stained positively and/or negatively for apoptotic markers cleaved caspase-3 and cleaved PARP, following DNA damage treatments induced by doxorubicin and TNF-alpha co-treatments

The present dataset contains the source data for Figure 2B of Tentner et al. (2012). The data shows the percentage of cultured cell-populations that stained positively and/or negatively for apoptotic markers cleaved caspase-3 and cleaved PARP, following DNA damage treatments induced by various doses of doxorubicin (0, 2 and 10 µmole/L) in the presence (100 ng/mL) or absence (0 ng/mL) of TNF-alpha co-treatment. For the six treatment conditions investigated, cell counts were made by flow cytometry at times 6, 12, 24, and 48 h following treatment; CULTURE DETAILS: U2OS cells were obtained from ATCC were maintained at 21% oxygen and 5% CO2 in Dulbecco's modified Eagle medium supplemented with 10% fetal bovine serum, penicillin, streptomycin, 2mM L-glutamine, and used within 15-20 passages. The first thymidine block was released by washing the plates three times with PBS, and incubating them in fresh thymidine-free media for 12 h. A second thymidine block was then performed by re-addition of thymidine to 2.5 mM followed by incubation for an additional 18 h. Media was aspirated, plates were washed 3 with PBS, and replaced with fresh media in the presence or absence of 10 mM aphidicolin; ANALYSIS DETAILS: See supplementary journal publication; RESULT: The authors of the supplementary journal publication conclude that TNF enhances dose-dependent cell death following doxorubicin-induced DNA damage with minimal affect on dose-dependent cell-cycle arrest.

Properties and faunal abundances of level sea ice and sea-ice ridges in the Chukchi/Beaufort Seas and Canada Basin

The abundances and distribution of metazoan within-ice meiofauna (13 stations) and under-ice fauna (12 stations) were investigated in level sea ice and sea-ice ridges in the Chukchi/Beaufort Seas and Canada Basin in June/July 2005 using a combination of ice coring and SCUBA diving. Ice meiofauna abundance was estimated based on live counts in the bottom 30 cm of level sea ice based on triplicate ice core sampling at each location, and in individual ice chunks from ridges at four locations. Under-ice amphipods were counted in situ in replicate (N=24-65 per station) 0.25 m**2 quadrats using SCUBA to a maximum water depth of 12 m. In level sea ice, the most abundant ice meiofauna groups were Turbellaria (46%), Nematoda (35%), and Harpacticoida (19%), with overall low abundances per station that ranged from 0.0 to 10.9 ind/l (median 0.8 ind/l). In level ice, low ice algal pigment concentrations (<0.1-15.8 µg Chl a /l), low brine salinities (1.8-21.7) and flushing from the melting sea ice likely explain the low ice meiofauna concentrations. Higher abundances of Turbellaria, Nematoda and Harpacticoida also were observed in pressure ridges (0-200 ind/l, median 40 ind/l), although values were highly variable and only medians of Turbellaria were significantly higher in ridge ice than in level ice. Median abundances of under-ice amphipods at all ice types (level ice, various ice ridge structures) ranged from 8 to 114 ind/m**2 per station and mainly consisted of Apherusa glacialis (87%), Onisimus spp. (7%) and Gammarus wilkitzkii (6%). Highest amphipod abundances were observed in pressure ridges at depths >3 m where abundances were up to 42-fold higher compared with level ice. We propose that the summer ice melt impacted meiofauna and under-ice amphipod abundance and distribution through (a) flushing, and (b) enhanced salinity stress at thinner level sea ice (less than 3 m thickness). We further suggest that pressure ridges, which extend into deeper, high-salinity water, become accumulation regions for ice meiofauna and under-ice amphipods in summer. Pressure ridges thus might be crucial for faunal survival during periods of enhanced summer ice melt. Previous estimates of Arctic sea ice meiofauna and under-ice amphipods on regional and pan-Arctic scales likely underestimate abundances at least in summer because they typically do not include pressure ridges.

Fork lengths, stomach contents and parasites of ninespine stickleback and arctic char in Iqalugaajuruluit Lake, Canada

Stable d13C and d15N isotopes, diet and parasites demonstrated that the prey consumed by ninespine stickleback Pungitius pungitius in a small lake on Baffin Island changed during the summer and also revealed intraspecific variation in their ecological niche. In July, there were differences in the diets of male and female ninespine stickleback as indicated by the stable isotopes, differences corroborated by the data on diet composition and the parasite fauna. Differences suggested that the sexes occupied different habitats during spawning. During July, females utilise the shallower littoral areas consuming zooplankton and benthic organisms, while males occupy deeper areas of the littoral zone feeding mainly on pelagic zooplankton. Parasite data support these observations as males had higher infections of copepod-transmitted parasites than females. There appeared to be no segregation of resources between males and females in late August, although the diet of both male and female ninespine stickleback shifted towards more benthic organisms, compared with July. Differences in d13C isotope, diet composition and infections of co-occurring parasites demonstrated that sympatric ninespine stickleback and Arctic char Salvelinus alpinus captured in the littoral zone occupied separate niches. Ninespine stickleback preyed mainly on zooplankton and chironomids, while Arctic char consumed a greater variety of prey items, including zooplankton and larger-sized prey such as insects and ninespine stickleback. The multifaceted approach improved our understanding of the trophic ecology of ninespine stickleback in southern Baffin Island and quantified resource use and dietary overlap with Arctic char.

Average nutrient concentration, and growth characteristics of bacteria during USCGC Healy cruises in 2002 and 2004

Standing stocks and production rates for phytoplankton and heterotrophic bacteria were examined during four expeditions in the western Arctic Ocean (Chukchi Sea and Canada Basin) in the spring and summer of 2002 and 2004. Rates of primary production (PP) and bacterial production (BP) were higher in the summer than in spring and in shelf waters than in the basin. Most surprisingly, PP was 3-fold higher in 2004 than in 2002; ice-corrected rates were 1581 and 458 mg C/m**2/d respectively, for the entire region. The difference between years was mainly due to low ice coverage in the summer of 2004. The spatial and temporal variation in PP led to comparable variation in BP. Although temperature explained as much variability in BP as did PP or phytoplankton biomass, there was no relationship between temperature and bacterial growth rates above about 0°C. The average ratio of BP to PP was 0.06 and 0.79 when ice-corrected PP rates were greater than and less than 100 mg C/m**2/d, respectively; the overall average was 0.34. Bacteria accounted for a highly variable fraction of total respiration, from 3% to over 60% with a mean of 25%. Likewise, the fraction of PP consumed by bacterial respiration, when calculated from growth efficiency (average of 6.9%) and BP estimates, varied greatly over time and space (7% to >500%). The apparent uncoupling between respiration and PP has several implications for carbon export and storage in the western Arctic Ocean.

Electrical properties of basalts of ODP Sites 124-768 and 124-770

Conductivity of 54 basalt samples from ODP Sites 768 and 770 was measured as a function of temperature and fluid salinity. Porosity was also measured for all samples, and cation exchange capacity was measured for 46 of the samples. Porosity measurements indicated that porosity is underestimated for basalts like these, unless one uses extensive drying at high vacuum. At salinities greater than 29 ppt, and throughout the range of salinity and temperatures likely in situ, sample conductivity (Co) is controlled by porosity (phi) according to the Archie relation Co = 0.22*Cw phi*1-3 (orFF = 4.5/f1.3), where Cw is conductivity of the pore fluids and FF = Cw/CO is the formation factor. At lower salinity, clay-surface conduction or microcrack conduction may dominate. We are unable to distinguish reliably between the two mechanisms, but we do detect their effects subtly at high salinity and strongly at low salinity.

Contribution of woody habitat islands to the conservation of birds and their potential ecosystem services in an extensive Colombian rangeland

The conservation of birds and their habitats is essential to maintain well-functioning ecosystems including human-dominated habitats. In simplified or homogenized landscapes, patches of natural and semi-natural habitat are essential for the survival of plant and animal populations. We compared species composition and diversity of trees and birds between gallery forests, tree islands and hedges in a Colombian savanna landscape to assess how fragmented woody plant communities affect forest bird communities and how differences in habitat characteristics influenced bird species traits and their potential ecosystem function. Bird and tree diversity was higher in forests than in tree islands and hedges. Soil depth influenced woody species distribution, and canopy cover and tree height determined bird species distribution, resulting in plant and bird communities that mainly differed between forest and non-forest habitat. Bird and tree species and traits widely co-varied. Bird species in tree islands and hedges were on average smaller, less specialized to habitat and more tolerant to disturbance than in forest, but dietary differences did not emerge. Despite being less complex and diverse than forests, hedges and tree islands significantly contribute to the conservation of forest biodiversity in the savanna matrix. Forest fragments remain essential for the conservation of forest specialists, but hedges and tree islands facilitate spillover of more tolerant forest birds and their ecological functions such as seed dispersal from forest to the savanna matrix.

Noble metals and associated trace elements in sulfides from the active TAG mound, ODP Site 158-957

Primary sulfides from cores of ODP Holes 158-957M, 158-957C, and 158-957H on the active TAG hydrothermal mound (Mid-Atlantic Ridge, 26°08'N) have been studied for concentrations of several chemical elements. Based on 262 microprobe analyses it has been found that the sulfides have extremely heterogeneous distribution of noble metals (Au, Ag, Pt, and Pd) and several associated elements (Hg, Co, and Se). Noble metals are arranged in the following order in terms of decreasing abundance, i.e. concentration level above detection limits (the number of analyses containing a specific element is given in parentheses): Au (65), Ag (46), Pt (21), and Pd (traces). The associated trace elements have the following series: Co (202), Hg (132), and Se (49). The main carriers of "invisible" portion of the noble metals are represented by pyrite (Au, Hg), marcasite and pyrite (Ag, Co), sphalerite and chalcopyrite (Pt, Pd), and chalcopyrite (Se). Noble metal distribution in sulfides reveals a lateral zonality: maximal concentrations and abundance of Au in chalcopyrite (or Pt and Ag in chalcopyrite and pyrite) increase from the periphery (Hole 957H) to the center (holes 957C and 957M) of the hydrothermal mound, while Au distribution in pyrite displays a reversed pattern. Co concentration increases with depth. Vertical zonality in distribution of the elements mentioned above and their response to evolution of ore genesis are under discussion in the paper.

Sedimentology and geochemistry of the sand fraction in surface sediments off West Africa

Surface sediments from 5 profiles between 30 and 3000 m water depth off W Africa (12-19° N) have been studied for their sand fraction composition and their total calcium carbonate and organic matter contents to evaluate the effect of climatic and hydrographic factors on actual sedimentation. On the shelf and upper slope (< 500 m), currents prevent the deposition of significant amounts of fine-grained material. The sediments forming here are characterized by high sand contents (> 60 %; in most samples > 89 %), low organic carbon contents (in most samples < 0.8 %), high median diameters of the sand fraction (120-500 µm), and by a predominance of quartz and biogenic relict shells (most abundant: molluscs and bryozoans) in the sand fraction. Median diameters of total sand fraction and of major biogenic sand fraction components (biogenic relict material, benthonic molluscs, benthonic and planktonic foraminifers) co-vary to some extent and show maximum values in 100-300 m water depth, reflectingthe sorting effect of currents (perhaps the northward flowing undercurrent). In this water depth, biogenic relict material is considerably enriched relative to wuartz, the second dominating sand fraction component on the shelf and upper slope, resulting in distinct calcium carbonate maxima of the bulk sediments. The influence of the undercurrent is also reflected in a northward transport of fine grained river load and perhaps in the distribution of the red stained, coarse silt and sand-size clay aggregates, which show maxima in 300-500 m water depth. They probably originate from tropical soils. Abundant coarse red-stained quartz on the shelf off Cape Roxo (12-130° N) suggests a southward extension of last glacial dune fields to this latitude. Below about 500 m water depth, current influence becomes negligible - as indicated by a strong decrease in sand content, a concomitant increase in sedimentary organic carbon contents (up to 2.5-3.5 %), and the occurence of high mica/quartz ratios in the sand fraction. Downslope transport, presumably due to the bioturbation mechanism, is indicated by the presence of coarse shelf-borne particles (glauconite, relict shells) down to about 1000 m water depth. The fine/coarse ratio (clay + silt/sand) of the sediments from water deoth > 500 m never exceed a value of 11 in northern latitudes (19° - 26° N), but shows distinct maxima, ranging from 50 to 120, at latitudes 18°, 17° 15°30', and 14° N in about 2000 m water depth. This distribution is attributed to the deposition of fine-grained river load at the continental slope between 18° and 14° N, brought into the sea by the Senegal and souther rivers and transported northward ny the undercurrent. Strong calcium carbonate dissolution is indicated by the complete disappearance of pteropodes (aragonite) and high fragmentation of the planktoic foraminifers (calcite) in sediments from water depth > 300-600 m. Fragmentation ratios of planktonic foraminifers were found to depend on the organic carbon/carbonate ratios of the sediment suggesting that calcite dissolution at the sea bottom may also be significant in shelf and continental slope water depths if the organic matter/carbonate ratio of the surface sediment is high and the test remain long enough within the oxidizing layer on the top of the sulfate reduction zone. The fact that in the region under study intensity and anual duration of upwelling decrease from north to south is neither reflected in the composition on the sand fraction (i.e. radiolarian and fish debris contents, radiolarian/planktonic foraminiferal ratios, benthos/plankton ratios of foraminifers), nor in the sedimentary organic carbon distribution. On the contrary, these parameters even show in comparable water depths a tendency for highest values in the south, partly because primary production rates remain high in the whole region, particularly on the shelf, due to the nutrient input by rivers in the south. In addition, several hydrographic, sedimentological and climatic factors severely affect their distribution - for example currents, dissolution, grain size composition, deposition of river load, and bulk sedimentation rats.

Analysis of Pacific oyster larval proteome and its response to high-CO2

Most calcifying organisms show depressed metabolic, growth and calcification rates as symptoms to high-CO(2) due to ocean acidification (OA) process. Analysis of the global expression pattern of proteins (proteome analysis) represents a powerful tool to examine these physiological symptoms at molecular level, but its applications are inadequate. To address this knowledge gap, 2-DE coupled with mass spectrophotometer was used to compare the global protein expression pattern of oyster larvae exposed to ambient and to high-CO(2). Exposure to OA resulted in marked reduction of global protein expression with a decrease or loss of 71 proteins (18% of the expressed proteins in control), indicating a wide-spread depression of metabolic genes expression in larvae reared under OA. This is, to our knowledge, the first proteome analysis that provides insights into the link between physiological suppression and protein down-regulation under OA in oyster larvae.

Gas hydrate structures and C1-C5 hydrocarbons at individual sites in the Gulf of Mexico

Gas hydrate samples from various locations in the Gulf of Mexico (GOM) differ considerably in their microstructure. Distinct microstructure characteristics coincide with discrete crystallographic structures, gas compositions and calculated thermodynamic stabilities. The crystallographic structures were established by X-ray diffraction, using both conventional X-ray sources and high-energy synchrotron radiation. The microstructures were examined by cryo-stage Field-Emission Scanning Electron Microscopy (FE-SEM). Good sample preservation was warranted by the low ice fractions shown from quantitative phase analyses. Gas hydrate structure II samples from the Green Canyon in the northern GOM had methane concentrations of 70-80% and up to 30% of C2-C5 of measured hydrocarbons. Hydrocarbons in the crystallographic structure I hydrate from the Chapopote asphalt volcano in the southern GOM was comprised of more than 98% methane. Fairly different microstructures were identified for those different hydrates: Pores measuring 200-400 nm in diameter were present in structure I gas hydrate samples; no such pores but dense crystal surfaces instead were discovered in structure II gas hydrate. The stability of the hydrate samples is discussed regarding gas composition, crystallographic structure and microstructure. Electron microscopic observations showed evidence of gas hydrate and liquid oil co-occurrence on a micrometer scale. That demonstrates that oil has direct contact to gas hydrates when it diffuses through a hydrate matrix.

Chemical and isotope composition of poor fluid from gas-hydrate samples of ODP Site 146-892

Although the presence of extensive gas hydrate on the Cascadia margin, offshore from the western U.S. and Canada, has been inferred from marine seismic records and pore water chemistry, solid gas hydrate has only been found at one location. At Ocean Drilling Program (ODP) Site 892, offshore from central Oregon, gas hydrate was recovered close to the sediment-water interface at 2-19 m below the seafloor (mbsf) at 670 m water depth. The gas hydrate occurs as elongated platy crystals or crystal aggregates, mostly disseminated irregularly, with higher concentrations occurring in discrete zones, thin layers, and/or veinlets parallel or oblique to the bedding. A 2- to 3-cm thick massive gas hydrate layer, parallel to bedding, was recovered at ~17 mbsf. Gas from a sample of this layer was composed of both CH4 and H2S. This sample is the first mixed-gas hydrate of CH4-H2S documented in ODP; it also contains ethane and minor amounts of CO2. Measured temperatures of the recovered core ranged from 2 to -1.8°C and are 6 to 8 degrees lower than in-situ temperatures. These temperature anomalies were caused by the partial dissociation of the CH4-H2S hydrate during recovery without a pressure core sampler. During this dissociation, toxic levels of H2S (delta34S, +27.4?) were released. The delta13C values of the CH4 in the gas hydrate, -64.5 to -67.5? (PDB), together with deltaD values of -197 to -199? (SMOW) indicate a primarily microbial source for the CH4. The delta18O value of the hydrate H2O is +2.9? (SMOW), comparable with the experimental fractionation factor for sea-ice. The unusual composition (CH4-H2S) and depth distribution (2-19 mbsf) of this gas hydrate indicate mixing between a methane-rich fluid with a pore fluid enriched in sulfide; at this site the former is advecting along an inclined fault into the active sulfate reduction zone. The facts that the CH4-H2S hydrate is primarily confined to the present day active sulfate reduction zone (2-19 mbsf), and that from here down to the BSR depth (19-68 mbsf) the gas hydrate inferred to exist is a >=99% CH4 hydrate, suggest that the mixing of CH4 and H2S is a geologically young process. Because the existence of a mixed CH4-H2S hydrate is indicative of moderate to intense advection of a methane-rich fluid into a near surface active sulfate reduction zone, tectonically active (faulted) margins with organic-rich sediments and moderate to high sedimentation rates are the most likely regions of occurrence. The extension of such a mixed hydrate below the sulfate reduction zone should reflect the time-span of methane advection into the sulfate reduction zone.

Seawater carbonate chemistry, nutrients, chlorophyll and diatom Proboscia alata during experiments, 2012

The combined effects of different light and aqueous CO2 conditions were assessed for the Southern Ocean diatom Proboscia alata(Brightwell) Sundström in laboratory experiments. Selected culture conditions (light and CO2(aq)) were representative for the natural ranges in the modern Southern Ocean. Light conditions were 40 (low) and 240 (high) µmol photons/m**2/s. The three CO2(aq) conditions ranged from 8 to 34 µmol/kg CO2(aq) (equivalent to a pCO2 from 137 to 598 µatm, respectively). Clear morphological changes were induced by these different CO2(aq) conditions. Cells in low [CO2(aq)] formed spirals, while many cells in high [CO2(aq)] disintegrated. Cell size and volume were significantly affected by the different CO2(aq) concentrations. Increasing CO2(aq) concentrations led to an increase in particulate organic carbon concentrations per cell in the high light cultures, with exactly the opposite happening in the low light cultures. However, other parameters measured were not influenced by the range of CO2(aq) treatments. This included growth rates, chlorophyll aconcentration and photosynthetic yield (FV/FM). Different light treatments had a large effect on nutrient uptake. High light conditions caused an increased nutrient uptake rate compared to cells grown in low light conditions. Light and CO2 conditions co-determined in various ways the response of P. alata to changing environmental conditions. Overall P. alata appeared to be well adapted to the natural variability in light availability and CO2(aq) concentration of the modern Southern Ocean. Nevertheless, our results showed that P. alata is susceptible to future changes in inorganic carbon concentrations in the Southern Ocean.

Tidal and spatial variations of DI13C and aquatic chemistry in a temperate tidal basin during winter time

Here, the pelagic carbonate system and the ?13C signature of dissolved inorganic carbonate (DIC) were investigated in a tidal basin of the southern North Sea, the Jade Bay, with respect to tidal cycles and a transect towards the North Sea in winter time (January and November, 2010). Physical parameters, major and trace elements, and nutrient concentrations were considered, too. Primary production and pelagic organic matter respiration were negligible during winter time. Both, the compositional variations on the transects as well as during the tidal cycles indicate the mixing of North Sea with fresh water. The combined spatial co-variations of different parameters indicate an introduction of fresh water that was enriched in DI12C, metabolites (e.g., ammonia), protons, and dissolved redox-sensitive elements (e.g., Mn2+). During the January campaign, the discharge via the flood gates was limited due to ice cover of the hinterland drainage ditches, allowing for an observation of tidal variations without significant mixing contributions from surface water discharges. Considering a binary mixing model with North Sea and fresh water as end-members, the extrapolated fresh water end-member composition for this campaign is estimated to contain about 3.8 mmol/kg DIC , and enhanced concentrations of NH4+, Mn2+, and protons compared to North Sea water. The fast temporal response of dissolved geochemical tracers on tidal variations in the Jade Bay indicates a continuous supply of a fresh water component. The measured composition of fresh waters entering the Jade Bay via flood gates (end of October, 2010) did not match the values estimated by the binary mixing model. Therefore, the overall fresh water component likely is a mixture between sources originating from flood gates and (in January) dominating submarine groundwater discharge entering the Jade Bay. This model is consistent with the results obtained during the November campaign, when a more important contribution from flood gates is expected and a more variable fresh water end-member is estimated. The co-variations of the concentrations and the stable carbon isotope composition of DIC are applied to evaluate possible superimposed sink-source-transformation processes in the coastal waters and a general co-variation scheme is suggested.

Plant species, biomass and environmental characteristics of relevés along the North America Arctic bioclimate gradient

Question: How do interactions between the physical environment and biotic properties of vegetation influence the formation of small patterned-ground features along the Arctic bioclimate gradient? Location: At 68° to 78°N: six locations along the Dalton Highway in arctic Alaska and three in Canada (Banks Island, Prince Patrick Island and Ellef Ringnes Island). Methods: We analysed floristic and structural vegetation, biomass and abiotic data (soil chemical and physical parameters, the n-factor [a soil thermal index] and spectral information [NDVI, LAI]) on 147 microhabitat releves of zonalpatterned-ground features. Using mapping, table analysis (JUICE) and ordination techniques (NMDS). Results: Table analysis using JUICE and the phi-coefficient to identify diagnostic species revealed clear groups of diagnostic plant taxa in four of the five zonal vegetation complexes. Plant communities and zonal complexes were generally well separated in the NMDS ordination. The Alaska and Canada communities were spatially separated in the ordination because of different glacial histories and location in separate floristic provinces, but there was no single controlling environmental gradient. Vegetation structure, particularly that of bryophytes and total biomass, strongly affected thermal properties of the soils. Patterned-ground complexes with the largest thermal differential between the patterned-ground features and the surrounding vegetation exhibited the clearest patterned-ground morphologies.

Paleomagnetic and age determinations on rocks from Nares Strait

The Nares Strait controversy concerns the debate about whether or not a major sinistral transcurrent fault (the Wegener Fault) separates northern Greenland and Canada. To date no firm evidence has been found for the proposed 200 km sinistral offset, and to the contrary, geological correlations, mainly involving Paleozoic rocks across the Nares Strait, suggest that total left-lateral motion is no more than 70 km. The E-W trending Thule (Greenland) and Devon Island (Canada) dyke swarms lie on opposite sides of Baffin Bay and are offset sinistrally about 200 km, suggesting that if their correlation is established a convincing case for the Wegener Fault can be made. Paleomagnetic, geochemical and petrographic data allow, but do not yet establish, the correlation. Paleomagnetic results for Canadian sites (VGP = 6.9°N, 181.8 °E, A95 = 12.7°, N = 5) and Greenland sites (VGP = 11.5 °N, 178.3 °E, A95 = 13.8°, N = 4) are not significantly different at the 95 % confidence level. These levels are too large to resolve whether or not the Thule and Devon Island swarms have been offset. Geochemical data reveal a distinct and identical pattern in incompatible elements, while petrographically, the dykes are indistinguishable. U-Pb geochronological results for a Canadian dyke (720.2 ±2.0 Ma) and a Thule dyke (720.4 ±2.7 Ma) are identical within error and clearly identify the two sets of dykes as being parts of the same magmatic episode.