Description: Experiments were conducted from 4 June to September 2007 inside laboratory facilities at the south coast of Madeira (32°38'N, 16°54'W). The organisms used for this study were the sea urchin Paracentrotus lividus collected at Doca do Cavacas (32° 38'06 N; 16° 56'52 W), the red seaweed Grateloupia imbricata collected from the marina of Funchal (32° 38'41 N; 16° 54'46 W) at 0.5 m water depth, and the brown seaweed Stypopodium zonale collected from boulders at Reis Magos, Caniço (32° 83'45 N; 16° 49'25 W) in water depths of 3-7 m. The study consisted of three sequential stages: (i) assessing algal light compensation points, (ii) inducing light limitation and grazing, (iii) assessing grazer consumption rates in no-choice feeding assays after light limitation and grazer impact. For the latter we used the algal material from stage (ii) (see additional file 1). Pilot studies were carried out in June 2007 to identify the Light Compensation Point (LCP) for both algal species, i.e. the light intensity at which the rate of photosynthesis (measured as oxygen production) equals respiration. For this, we reduced the amount of incoming light by placing various layers of black plastic gauze material with a mesh size of 1 mm on top of each aquarium. For both macroalgae, we had a total of 12 aquaria (3.5 L each) of with each was loaded with 30 - 40 g wet weight of seaweed material. We randomly assigned two aquaria to each of six different light regimes. The number of gauze layers used was 0, 1, 2, 3, 4 and 5. After we recorded the concentration of dissolved oxygen with an oxymeter (Oxi 197, WTW Wissenschaftlich-Technische Werkstätten GmbH, Weilheim, Germany) twice a day (9am and 5pm) for the following 4 days (see additional file 2). Experiments were carried out in July 2007 for G. imbricata, and in September 2007 for S. zonale. We conducted a two-factorial experiment for each of the species in which we crossed two levels of grazing ("grazed" and "non-grazed") with six levels of light intensities (0-5 layers of gauze material) and each treatment combination was replicated eight times (n=8). Consequently, we had 6 x 8 = 48 aquaria of which each contained one sea urchin, while another 48 aquaria had no sea urchins. The latter were used to determine total algal growth rates under the different light regimes in the absence of grazers and to provide non-grazed algal material for the feeding assays. In total we had 96 aquaria for each of the two seaweed species in the study and the respective treatments, i.e. light limitation and grazing, were imposed simultaneously for 21 days. We tested for possible effects of the previously applied light limitation and grazing (see stage (ii)) on grazer consumption rates in no-choice feeding assays that lasted for 24 h. Hence, the number of replicates for the assays at stage (iii) was the same as at stage (ii). Grazer consumption rates of algal material were determined as the grazers' total consumption, which was calculated using the equation suggested by Cronin and Hay (1996-a): [Ai x (Cf / Ci) - Af ] where Ai and Af were the initial and final weight of the algae portions used in the feeding assays; Ci and Cf are the equivalent weights of the growth control algal pieces before and after the assays (Sotka et al., 2002). Finally, consumption rates were standardised for grazer wet biomass (g alga/g grazer). Negative consumption was recorded in case algal growth rates during the assays exceeded consumption rates (see additional file 3 raw data).

Description: Seamounts are amongst the most common physiographic structures of the deep-ocean landscape, but remoteness and geographic complexity have limited the systematic collection of integrated and multidisciplinary data in the past. Consequently, important aspects of seamount ecology and dynamics remain poorly studied. We present a data collection of ocean currents and raw acoustic backscatter from shipboard Acoustic Doppler Current Profiler (ADCP) measurements during six cruises between 2004 and 2015 in the tropical and subtropical Northeast Atlantic to narrow this gap. Measurements were conducted at seamount locations between the island of Madeira and the Portuguese mainland (Ampère, Seine Seamount), as well as east of the Cape Verde archipelago (Senghor Seamount). The dataset includes two-minute ensemble averaged continuous velocity and backscatter profiles, supplemented by spatially gridded maps for each velocity component, error velocity and local bathymetry.

Description: It has been suggested that non-native species are more tolerant towards abiotic stress than ecologically comparable native species. Furthermore, non-native marine macroalgae should be under lower grazing pressure than native seaweeds, because they left their co-evolved enemies behind. As a consequence, they generally need to allocate less energy to defences and can invest more into compensating the negative effects of abiotic stress or, assuming that grazing pressure is low but not zero, to defensive reactions following grazer attack. This, in turn, should make them more stress tolerant and less susceptible to herbivory. However, empirical evidence for both concepts is still scarce and very little is known about whether enemy release is commonly associated with an enhanced tolerance towards abiotic or biotic stress. We therefore ran an experimental study that (a) assessed attractiveness for grazers, (b) verified whether short-term low-light stress impairs growth and (c) investigated whether light limitation and previous grazing interactively affect the consumption of two macroalgae from Madeira Island, the native brown alga Stypopodium zonale and the non-native red alga Grateloupia imbricata by the sea urchin Paracentrotus lividus. To come to ecologically meaningful low-light stress levels, pilot studies were performed in order to determine the light compensation point of photosynthesis for each algal species and then we established six light regimes around this point by reducing the amount of incoming light. Simultaneously, we let one sea urchin graze on each algal individual to stimulate a chemical defence in the seaweeds if present. In parallel to this, we kept the same number of algal replicates in the absence of sea urchins. After 21 days, we compared algal growth in the absence of grazers as well as the attractiveness of previously grazed and non-grazed algal material for P. lividus across all light regimes. Algal attractiveness was assessed in no-choice feeding assays. The observation that the non-native alga was less consumed by the grazer than the native species generally confirms the concept of enemy release. However, light limitation reduced growth in the non-native but not in the native seaweed, while previous grazing reduced consumption of the native but enhanced it in case of the non-native alga. These findings do not corroborate the assumption that enemy release can, through the re-allocation of energy, enhance tolerance to abiotic (light limitation) or biotic (grazing) stressors in non-native marine macroalgae.

Description: This paper presents new data sets relating to the abundance of atomic oxygen in the upper mesosphere and lower thermosphere, which were derived from the nighttime green line emission measurements of the SCIAMACHY (Scanning Imaging Absorption Spectrometer for Atmospheric CHartographY) instrument on the European Environmental Satellite (Envisat). These are compared to recently published data sets from the same SCIAMACHY green line measurements through the application of a different photochemical model and to data collected by the SABER (Sounding of the Atmosphere using Broadband Emission Radiometry) instrument. We find that the retrieved atomic oxygen concentration depends on the choice of the underlying photochemical model. These dependencies explain a large proportion of the differences between recently published data sets. The impact of the 11-year solar cycle on volume emission rates and atomic oxygen abundances was analyzed for various data sets, with the finding that the solar cycle effect varies with the atomic oxygen data set used. The solar cycle impact on the SCIAMACHY data increases with altitude. Above 96 km, it is significantly larger than predicted by HAMMONIA (Hamburg Model of the Neutral and Ionized Atmosphere). Investigations indicate that these variations are primarily driven by total density compression/expansion variations during the solar cycle, rather than different photolysis rates.

Description: Cancer is a large class of diseases that are characterized by a common set of features, known as the Hallmarks of Cancer . One of these hallmarks is the acquisition of genome instability and mutations. This, combined with high proliferation rates and failure of repair mechanisms, leads to clonal evolution as well as a high genotypic and phenotypic diversity within the tumor. As a consequence, treatment and therapy of malignant tumors is still a grand challenge. Moreover, under selective pressure, e.g. caused by chemotherapy, resistant subpopulations can emerge that then may lead to relapse. In order to minimize the risk of developing multi-drug resistant tumor cell populations, optimal (combination) therapies have to be determined on the basis of an in-depth characterization of the tumor's genetic and phenotypic makeup, a process which is an important aspect of stratified medicine and precision medicine. We present DrugTargetInspector (DTI), an interactive assistance tool for treatment stratification. DTI analyzes genomic, transcriptomic and proteomic datasets and provides information on deregulated drug targets, enriched biological pathways and deregulated subnetworks, as well as mutations and their potential effects on putative drug targets and genes of interest. To demonstrate DTI's broad scope of applicability, we present case studies on several cancer types and different types of input -omics data. DTI's integrative approach allows users to characterize the tumor under investigation based on various -omics datasets and to elucidate putative treatment options based on clinical decision guidelines, but also proposing additional points of intervention that might be neglected otherwise. DTI can be freely accessed at http://dti.bioinf.uni-sb.de . This article is protected by copyright. All rights reserved.