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Background:
Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked
to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research
comprising manifold, diverse and time
‑consuming experiments, the findings can be fostered by reusing and combin‑
ing existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible
provided that the collected observations are equipped with an adequate set of metadata. So far there have been no
common standards governing phenotypic data description, which hampered data exchange and reuse.
Results:
In this paper we propose the guidelines for proper handling of the information about plant phenotyping
experiments, in terms of both the recommended content of the description and its formatting. We provide a docu‑
ment called “Minimum Information About a Plant Phenotyping Experiment”, which specifies what information about
each experiment should be given, and a Phenotyping Configuration for the ISA
‑Tab format, which allows to practically
organise this information within a dataset. We provide examples of ISA
‑Tab
‑formatted phenotypic data, and a general
description of a few systems where the recommendations have been implemented.
Conclusions:
Acceptance of the rules described in this paper by the plant phenotyping community will help to
achieve findable, accessible, interoperable and reusable data.
Unlike for other retroviruses, only a few host cell factors that aid the replication of foamy viruses (FVs) via interaction with viral structural components are known. Using a yeast-two-hybrid (Y2H) screen with prototype FV (PFV) Gag protein as bait we identified human polo-like kinase 2 (hPLK2), a member of cell cycle regulatory kinases, as a new interactor of PFV capsids. Further Y2H studies confirmed interaction of PFV Gag with several PLKs of both human and rat origin. A consensus Ser-Thr/Ser-Pro (S-T/S-P) motif in Gag, which is conserved among primate FVs and phosphorylated in PFV virions, was essential for recognition by PLKs. In the case of rat PLK2, functional kinase and polo-box domains were required for interaction with PFV Gag. Fluorescently-tagged PFV Gag, through its chromatin tethering function, selectively relocalized ectopically expressed eGFP-tagged PLK proteins to mitotic chromosomes in a Gag STP motif-dependent manner, confirming a specific and dominant nature of the Gag-PLK interaction in mammalian cells. The functional relevance of the Gag-PLK interaction was examined in the context of replication-competent FVs and single-round PFV vectors. Although STP motif mutated viruses displayed wild type (wt) particle release, RNA packaging and intra-particle reverse transcription, their replication capacity was decreased 3-fold in single-cycle infections, and up to 20-fold in spreading infections over an extended time period. Strikingly similar defects were observed when cells infected with single-round wt Gag PFV vectors were treated with a pan PLK inhibitor. Analysis of entry kinetics of the mutant viruses indicated a post-fusion defect resulting in delayed and reduced integration, which was accompanied with an enhanced preference to integrate into heterochromatin. We conclude that interaction between PFV Gag and cellular PLK proteins is important for early replication steps of PFV within host cells.
The knowledge of the contemporary in situ stress state is a key issue for safe and sustainable subsurface engineering. However, information on the orientation and magnitudes of the stress state is limited and often not available for the areas of interest. Therefore 3-D geomechanical-numerical modelling is used to estimate the in situ stress state and the distance of faults from failure for application in subsurface engineering. The main challenge in this approach is to bridge the gap in scale between the widely scattered data used for calibration of the model and the high resolution in the target area required for the application. We present a multi-stage 3-D geomechanical-numerical approach which provides a state-of-the-art model of the stress field for a reservoir-scale area from widely scattered data records. Therefore, we first use a large-scale regional model which is calibrated by available stress data and provides the full 3-D stress tensor at discrete points in the entire model volume. The modelled stress state is used subsequently for the calibration of a smaller-scale model located within the large-scale model in an area without any observed stress data records. We exemplify this approach with two-stages for the area around Munich in the German Molasse Basin. As an example of application, we estimate the scalar values for slip tendency and fracture potential from the model results as measures for the criticality of fault reactivation in the reservoir-scale model. The modelling results show that variations due to uncertainties in the input data are mainly introduced by the uncertain material properties and missing S-Hmax magnitude estimates needed for a more reliable model calibration. This leads to the conclusion that at this stage the model's reliability depends only on the amount and quality of available stress information rather than on the modelling technique itself or on local details of the model geometry. Any improvements in modelling and increases in model reliability can only be achieved using more high-quality data for calibration.
Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.
The eukaryotic-specific Isd11 is a complex- orphan protein with ability to bind the prokaryotic IscS
(2016)
The eukaryotic protein Isd11 is a chaperone that binds and stabilizes the central component of the essential metabolic pathway responsible for formation of iron-sulfur clusters in mitochondria, the desulfurase Nfs1. Little is known about the exact role of Isd11. Here, we show that human Isd11 (ISD11) is a helical protein which exists in solution as an equilibrium between monomer, dimeric and tetrameric species when in the absence of human Nfs1 (NFS1). We also show that, surprisingly, recombinant ISD11 expressed in E. coli co-purifies with the bacterial orthologue of NFS1, IscS. Binding is weak but specific suggesting that, despite the absence of Isd11 sequences in bacteria, there is enough conservation between the two desulfurases to retain a similar mode of interaction. This knowledge may inform us on the conservation of the mode of binding of Isd11 to the desulfurase. We used evolutionary evidence to suggest Isd11 residues involved in the interaction.
In this study, we investigated the scale sizes of equatorial plasma irregularities (EPIs) using measurements from the Swarm satellites during its early mission and final constellation phases. We found that with longitudinal separation between Swarm satellites larger than 0.4°, no significant correlation was found any more. This result suggests that EPI structures include plasma density scale sizes less than 44 km in the zonal direction. During the Swarm earlier mission phase, clearly better EPI correlations are obtained in the northern hemisphere, implying more fragmented irregularities in the southern hemisphere where the ambient magnetic field is low. The previously reported inverted-C shell structure of EPIs is generally confirmed by the Swarm observations in the northern hemisphere, but with various tilt angles. From the Swarm spacecrafts with zonal separations of about 150 km, we conclude that larger zonal scale sizes of irregularities exist during the early evening hours (around 1900 LT).
Gut bacteria exert beneficial and harmful effects in metabolic diseases as deduced from the comparison of germfree and conventional mice and from fecal transplantation studies. Compositional microbial changes in diseased subjects have been linked to adiposity, type 2 diabetes and dyslipidemia. Promotion of an increased expression of intestinal nutrient transporters or a modified lipid and bile acid metabolism by the intestinal microbiota could result in an increased nutrient absorption by the host. The degradation of dietary fiber and the subsequent fermentation of monosaccharides to short-chain fatty acids (SCFA) is one of the most controversially discussed mechanisms of how gut bacteria impact host physiology. Fibers reduce the energy density of the diet, and the resulting SCFA promote intestinal gluconeogenesis, incretin formation and subsequently satiety. However, SCFA also deliver energy to the host and support liponeogenesis. Thus far, there is little knowledge on bacterial species that promote or prevent metabolic disease. Clostridium ramosum and Enterococcus cloacae were demonstrated to promote obesity in gnotobiotic mouse models, whereas bifidobacteria and Akkermansia muciniphila were associated with favorable phenotypes in conventional mice, especially when oligofructose was fed. How diet modulates the gut microbiota towards a beneficial or harmful composition needs further research. Gnotobiotic animals are a valuable tool to elucidate mechanisms underlying diet-host-microbe interactions.
Isostasy is one of the oldest and most widely applied concepts in the geosciences, but the geoscientific community lacks a coherent, easy-to-use tool to simulate flexure of a realistic (i.e., laterally heterogeneous) lithosphere under an arbitrary set of surface loads. Such a model is needed for studies of mountain building, sedimentary basin formation, glaciation, sea-level change, and other tectonic, geodynamic, and surface processes. Here I present gFlex (for GNU flexure), an open-source model that can produce analytical and finite difference solutions for lithospheric flexure in one (profile) and two (map view) dimensions. To simulate the flexural isostatic response to an imposed load, it can be used by itself or within GRASS GIS for better integration with field data. gFlex is also a component with the Community Surface Dynamics Modeling System (CSDMS) and Landlab modeling frameworks for coupling with a wide range of Earth-surface-related models, and can be coupled to additional models within Python scripts. As an example of this in-script coupling, I simulate the effects of spatially variable lithospheric thickness on a modeled Iceland ice cap. Finite difference solutions in gFlex can use any of five types of boundary conditions: 0-displacement, 0-slope (i.e., clamped); 0-slope, 0-shear; 0-moment, 0-shear (i.e., broken plate); mirror symmetry; and periodic. Typical calculations with gFlex require << 1 s to similar to 1 min on a personal laptop computer. These characteristics - multiple ways to run the model, multiple solution methods, multiple boundary conditions, and short compute time - make gFlex an effective tool for flexural isostatic modeling across the geosciences.
The coil-to-globule transition of poly(N-isopropylacrylamide) (PNIPAM) microgel particles suspended in water has been investigated in situ as a function of heating and cooling rate with four optical process analytical technologies (PAT), sensitive to structural changes of the polymer. Photon Density Wave (PDW) spectroscopy, Focused Beam Reflectance Measurements (FBRM), turbidity measurements, and Particle Vision Microscope (PVM) measurements are found to be powerful tools for the monitoring of the temperature-dependent transition of such thermo-responsive polymers. These in-line technologies allow for monitoring of either the reduced scattering coefficient and the absorption coefficient, the chord length distribution, the reflected intensities, or the relative backscatter index via in-process imaging, respectively. Varying heating and cooling rates result in rate-dependent lower critical solution temperatures (LCST), with different impact of cooling and heating. Particularly, the data obtained by PDW spectroscopy can be used to estimate the thermodynamic transition temperature of PNIPAM for infinitesimal heating or cooling rates. In addition, an inverse hysteresis and a reversible building of micrometer-sized agglomerates are observed for the PNIPAM transition process.
The advantages of remote sensing using Unmanned Aerial Vehicles (UAVs) are a high spatial resolution of images, temporal flexibility and narrow-band spectral data from different wavelengths domains. This enables the detection of spatio-temporal dynamics of environmental variables, like plant-related carbon dynamics in agricultural landscapes. In this paper, we quantify spatial patterns of fresh phytomass and related carbon (C) export using imagery captured by a 12-band multispectral camera mounted on the fixed wing UAV Carolo P360. The study was performed in 2014 at the experimental area CarboZALF-D in NE Germany. From radiometrically corrected and calibrated images of lucerne (Medicago sativa), the performance of four commonly used vegetation indices (VIs) was tested using band combinations of six near-infrared bands. The highest correlation between ground-based measurements of fresh phytomass of lucerne and VIs was obtained for the Enhanced Vegetation Index (EVI) using near-infrared band b(899). The resulting map was transformed into dry phytomass and finally upscaled to total C export by harvest. The observed spatial variability at field- and plot-scale could be attributed to small-scale soil heterogeneity in part.
Molecular paleoclimate reconstructions over the last 9 ka from a peat sequence in South China
(2016)
To achieve a better understanding of Holocene climate change in the monsoon regions of China, we investigated the molecular distributions and carbon and hydrogen isotope compositions delta C-13 and delta D values) of long-chain n-alkanes in a peat core from the Shiwangutian SWGT) peatland, south China over the last 9 ka. By comparisons with other climate records, we found that the delta C-13 values of the long-chain n-alkanes can be a proxy for humidity, while the dD values of the long-chain n-alkanes primarily recorded the moisture source dD signal during 9-1.8 ka BP and responded to the dry climate during 1.8-0.3 ka BP. Together with the average chain length ACL) and the carbon preference index CPI) data, the climate evolution over last 9 ka in the SWGT peatland can be divided into three stages. During the first stage 9-5 ka BP), the delta C-13 values were depleted and CPI and Paq values were low, while ACL values were high. They reveal a period of warm and wet climate, which is regarded as the Holocene optimum. The second stage 5-1.8 ka BP) witnessed a shift to relatively cool and dry climate, as indicated by the more positive delta C-13 values and lower ACL values. During the third stage 1.8-0.3 ka BP), the delta C-13, delta D, CPI and Paq values showed marked increase and ACL values varied greatly, implying an abrupt change to cold and dry conditions. This climate pattern corresponds to the broad decline in Asian monsoon intensity through the latter part of the Holocene. Our results do not support a later Holocene optimum in south China as suggested by previous studies.
Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae. Chloroflexi, and Therrnoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanornicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.
Introduction
Genes involved in body weight regulation that were previously investigated in genome-wide association studies (GWAS) and in animal models were target-enriched followed by massive parallel next generation sequencing.
Methods
We enriched and re-sequenced continuous genomic regions comprising FTO, MC4R, TMEM18, SDCCAG8, TKNS, MSRA and TBC1D1 in a screening sample of 196 extremely obese children and adolescents with age and sex specific body mass index (BMI) >= 99th percentile and 176 lean adults (BMI <= 15th percentile). 22 variants were confirmed by Sanger sequencing. Genotyping was performed in up to 705 independent obesity trios (extremely obese child and both parents), 243 extremely obese cases and 261 lean adults.
Results and Conclusion
We detected 20 different non-synonymous variants, one frame shift and one nonsense mutation in the 7 continuous genomic regions in study groups of different weight extremes. For SNP Arg695Cys (rs58983546) in TBC1D1 we detected nominal association with obesity (p(TDT) = 0.03 in 705 trios). Eleven of the variants were rare, thus were only detected heterozygously in up to ten individual(s) of the complete screening sample of 372 individuals. Two of them (in FTO and MSRA) were found in lean individuals, nine in extremely obese. In silico analyses of the 11 variants did not reveal functional implications for the mutations. Concordant with our hypothesis we detected a rare variant that potentially leads to loss of FTO function in a lean individual. For TBC1D1, in contrary to our hypothesis, the loss of function variant (Arg443Stop) was found in an obese individual. Functional in vitro studies are warranted.
In a network with a mixture of different electrophysiological types of neurons linked by excitatory and inhibitory connections, temporal evolution leads through repeated epochs of intensive global activity separated by intervals with low activity level. This behavior mimics "up" and "down" states, experimentally observed in cortical tissues in absence of external stimuli. We interpret global dynamical features in terms of individual dynamics of the neurons. In particular, we observe that the crucial role both in interruption and in resumption of global activity is played by distributions of the membrane recovery variable within the network. We also demonstrate that the behavior of neurons is more influenced by their presynaptic environment in the network than by their formal types, assigned in accordance with their response to constant current.
Injection of fluids into deep saline aquifers causes a pore pressure increase in the storage formation, and thus displacement of resident brine. Via hydraulically conductive faults, brine may migrate upwards into shallower aquifers and lead to unwanted salinisation of potable groundwater resources. In the present study, we investigated different scenarios for a potential storage site in the Northeast German Basin using a three-dimensional (3-D) regional-scale model that includes four major fault zones. The focus was on assessing the impact of fault length and the effect of a secondary reservoir above the storage formation, as well as model boundary conditions and initial salinity distribution on the potential salinisation of shallow groundwater resources. We employed numerical simulations of brine injection as a representative fluid.
Our simulation results demonstrate that the lateral model boundary settings and the effective fault damage zone volume have the greatest influence on pressure build-up and development within the reservoir, and thus intensity and duration of fluid flow through the faults. Higher vertical pressure gradients for short fault segments or a small effective fault damage zone volume result in the highest salinisation potential due to a larger vertical fault height affected by fluid displacement. Consequently, it has a strong impact on the degree of shallow aquifer salinisation, whether a gradient in salinity exists or the saltwater-freshwater interface lies below the fluid displacement depth in the faults. A small effective fault damage zone volume or low fault permeability further extend the duration of fluid flow, which can persist for several tens to hundreds of years, if the reservoir is laterally confined. Laterally open reservoir boundaries, large effective fault damage zone volumes and intermediate reservoirs significantly reduce vertical brine migration and the potential of freshwater salinisation because the origin depth of displaced brine is located only a few decametres below the shallow aquifer in maximum.
The present study demonstrates that the existence of hydraulically conductive faults is not necessarily an exclusion criterion for potential injection sites, because salinisation of shallower aquifers strongly depends on initial salinity distribution, location of hydraulically conductive faults and their effective damage zone volumes as well as geological boundary conditions.
Plasma carotenoids, tocopherols, and retinol in the age-stratified (35–74 years) general population
(2016)
Blood micronutrient status may change with age. We analyzed plasma carotenoids, α-/γ-tocopherol, and retinol and their associations with age, demographic characteristics, and dietary habits (assessed by a short food frequency questionnaire) in a cross-sectional study of 2118 women and men (age-stratified from 35 to 74 years) of the general population from six European countries. Higher age was associated with lower lycopene and α-/β-carotene and higher β-cryptoxanthin, lutein, zeaxanthin, α-/γ-tocopherol, and retinol levels. Significant correlations with age were observed for lycopene (r = −0.248), α-tocopherol (r = 0.208), α-carotene (r = −0.112), and β-cryptoxanthin (r = 0.125; all p < 0.001). Age was inversely associated with lycopene (−6.5% per five-year age increase) and this association remained in the multiple regression model with the significant predictors (covariables) being country, season, cholesterol, gender, smoking status, body mass index (BMI (kg/m2)), and dietary habits. The positive association of α-tocopherol with age remained when all covariates including cholesterol and use of vitamin supplements were included (1.7% vs. 2.4% per five-year age increase). The association of higher β-cryptoxanthin with higher age was no longer statistically significant after adjustment for fruit consumption, whereas the inverse association of α-carotene with age remained in the fully adjusted multivariable model (−4.8% vs. −3.8% per five-year age increase). We conclude from our study that age is an independent predictor of plasma lycopene, α-tocopherol, and α-carotene.
Low Earth orbiting geomagnetic satellite missions, such as the Swarm satellite mission, are the only means to monitor and investigate ionospheric currents on a global scale and to make in situ measurements of F region currents. High-precision geomagnetic satellite missions are also able to detect ionospheric currents during quiet-time geomagnetic conditions that only have few nanotesla amplitudes in the magnetic field. An efficient method to isolate the ionospheric signals from satellite magnetic field measurements has been the use of residuals between the observations and predictions from empirical geomagnetic models for other geomagnetic sources, such as the core and lithospheric field or signals from the quiet-time magnetospheric currents. This study aims at highlighting the importance of high-resolution magnetic field models that are able to predict the lithospheric field and that consider the quiet-time magnetosphere for reliably isolating signatures from ionospheric currents during geomagnetically quiet times. The effects on the detection of ionospheric currents arising from neglecting the lithospheric and magnetospheric sources are discussed on the example of four Swarm orbits during very quiet times. The respective orbits show a broad range of typical scenarios, such as strong and weak ionospheric signal (during day- and nighttime, respectively) superimposed over strong and weak lithospheric signals. If predictions from the lithosphere or magnetosphere are not properly considered, the amplitude of the ionospheric currents, such as the midlatitude Sq currents or the equatorial electrojet (EEJ), is modulated by 10–15 % in the examples shown. An analysis from several orbits above the African sector, where the lithospheric field is significant, showed that the peak value of the signatures of the EEJ is in error by 5 % in average when lithospheric contributions are not considered, which is in the range of uncertainties of present empirical models of the EEJ.
About a quarter of anthropogenic CO2 emissions are currently taken up by the oceans, decreasing seawater pH. We performed a mesocosm experiment in the Baltic Sea in order to investigate the consequences of increasing CO2 levels on pelagic carbon fluxes. A gradient of different CO2 scenarios, ranging from ambient (similar to 370 mu atm) to high (similar to 1200 mu atm), were set up in mesocosm bags (similar to 55m(3)). We determined standing stocks and temporal changes of total particulate carbon (TPC), dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), and particulate organic carbon (POC) of specific plankton groups. We also measured carbon flux via CO2 exchange with the atmosphere and sedimentation (export), and biological rate measurements of primary production, bacterial production, and total respiration. The experiment lasted for 44 days and was divided into three different phases (I: t0-t16; II: t17-t30; III: t31-t43). Pools of TPC, DOC, and DIC were approximately 420, 7200, and 25 200 mmol Cm-2 at the start of the experiment, and the initial CO2 additions increased the DIC pool by similar to 7% in the highest CO2 treatment. Overall, there was a decrease in TPC and increase of DOC over the course of the experiment. The decrease in TPC was lower, and increase in DOC higher, in treatments with added CO2. During phase I the estimated gross primary production (GPP) was similar to 100 mmol C m(-2) day(-1), from which 75-95% was respired, similar to 1% ended up in the TPC (including export), and 5-25% was added to the DOC pool. During phase II, the respiration loss increased to similar to 100% of GPP at the ambient CO2 concentration, whereas respiration was lower (85-95% of GPP) in the highest CO2 treatment. Bacterial production was similar to 30% lower, on average, at the highest CO2 concentration than in the controls during phases II and III. This resulted in a higher accumulation of DOC and lower reduction in the TPC pool in the elevated CO2 treatments at the end of phase II extending throughout phase III. The "extra" organic carbon at high CO2 remained fixed in an increasing biomass of small-sized plankton and in the DOC pool, and did not transfer into large, sinking aggregates. Our results revealed a clear effect of increasing CO2 on the carbon budget and mineralization, in particular under nutrient limited conditions. Lower carbon loss processes (respiration and bacterial remineralization) at elevated CO2 levels resulted in higher TPC and DOC pools than ambient CO2 concentration. These results highlight the importance of addressing not only net changes in carbon standing stocks but also carbon fluxes and budgets to better disentangle the effects of ocean acidification.
The hydrological budget of a region is determined based on the horizontal and vertical water fluxes acting in both inward and outward directions. These integrated water fluxes vary, altering the total water storage and consequently the gravitational force of the region. The time-dependent gravitational field can be observed through the Gravity Recovery and Climate Experiment (GRACE) gravimetric satellite mission, provided that the mass variation is above the sensitivity of GRACE. This study evaluates mass changes in prominent reservoir regions through three independent approaches viz. fluxes, storages, and gravity, by combining remote sensing products, in-situ data and hydrological model outputs using WaterGAP Global Hydrological Model (WGHM) and Global Land Data Assimilation System (GLDAS). The results show that the dynamics revealed by the GRACE signal can be better explored by a hybrid method, which combines remote sensing-based reservoir volume estimates with hydrological model outputs, than by exclusive model-based storage estimates. For the given arid/ semi-arid regions, GLDAS based storage estimations perform better than WGHM.
Ongoing climate change is known to cause an increase in the frequency and amplitude of local temperature and precipitation extremes in many regions of the Earth. While gradual changes in the climatological conditions have already been shown to strongly influence plant flowering dates, the question arises if and how extremes specifically impact the timing of this important phenological phase. Studying this question calls for the application of statistical methods that are tailored to the specific properties of event time series. Here, we employ event coincidence analysis, a novel statistical tool that allows assessing whether or not two types of events exhibit similar sequences of occurrences in order to systematically quantify simultaneities between meteorological extremes and the timing of the flowering of four shrub species across Germany. Our study confirms previous findings of experimental studies by highlighting the impact of early spring temperatures on the flowering of the investigated plants. However, previous studies solely based on correlation analysis do not allow deriving explicit estimates of the strength of such interdependencies without further assumptions, a gap that is closed by our analysis. In addition to direct impacts of extremely warm and cold spring temperatures, our analysis reveals statistically significant indications of an influence of temperature extremes in the autumn preceding the flowering.
Observed recent and expected future increases in frequency and intensity of climatic extremes in central Europe may pose critical challenges for domestic tree species. Continuous dendrometer recordings provide a valuable source of information on tree stem radius variations, offering the possibility to study a tree's response to environmental influences at a high temporal resolution. In this study, we analyze stem radius variations (SRV) of three domestic tree species (beech, oak, and pine) from 2012 to 2014. We use the novel statistical approach of event coincidence analysis (ECA) to investigate the simultaneous occurrence of extreme daily weather conditions and extreme SRVs, where extremes are defined with respect to the common values at a given phase of the annual growth period. Besides defining extreme events based on individual meteorological variables, we additionally introduce conditional and joint ECA as new multivariate extensions of the original methodology and apply them for testing 105 different combinations of variables regarding their impact on SRV extremes. Our results reveal a strong susceptibility of all three species to the extremes of several meteorological variables. Yet, the inter-species differences regarding their response to the meteorological extremes are comparatively low. The obtained results provide a thorough extension of previous correlation-based studies by emphasizing on the timings of climatic extremes only. We suggest that the employed methodological approach should be further promoted in forest research regarding the investigation of tree responses to changing environmental conditions.
Mountain and upland regions provide a wide range of ecosystem services to residents and visitors. While ecosystem research in mountain regions is on the rise, the linkages between sociocultural benefits and ecological systems remain little explored. Mountainous regions close to urban areas provide numerous benefits to a large number of individuals, suggesting a high social value, particularly for cultural ecosystem services. We explored and compared visitors' valuation of ecosystem services in the Pentland Hills, an upland range close to the city of Edinburgh, Scotland, and urban green spaces within Edinburgh. Based on 715 responses to user surveys in both study areas, we identified intense use and high social value for both areas. Several ecosystem services were perceived as equally important in both areas, including many cultural ecosystem services. Significant differences were revealed in the value of physically using nature, which Pentland Hills users rated more highly than those in the urban green spaces, and of mitigation of pollutants and carbon sequestration, for which the urban green spaces were valued more highly. Major differences were further identified for preferences in future land management, with nature-oriented management preferred by about 57% of the interviewees in the Pentland Hills, compared to 31% in the urban parks. The study highlights the substantial value of upland areas in close vicinity to a city for physically using and experiencing nature, with a strong acceptance of nature conservation.
Ecosystem services have a significant impact on human wellbeing. While ecosystem services are frequently represented by monetary values, social values and underlying social benefits remain under explored. The purpose of this study is to assess whether and how social benefits have been explicitly addressed within socio-economic and socio-cultural ecosystem services research, ultimately allowing a better understanding between ecosystem services and human well-being. In this paper, we reviewed 115 international primary valuation studies and tested four hypotheses associated to the identification of social benefits of ecosystem services using logistic regressions. Tested hypotheses were that (1) social benefits are mostly derived in studies that assess cultural ecosystem services as opposed to other ecosystem service types, (2) there is a pattern of social benefits and certain cultural ecosystem services assessed simultaneously, (3) monetary valuation techniques go beyond expressing monetary values and convey social benefits, and (4) directly addressing stakeholder's views the consideration of social benefits in ecosystem service assessments. Our analysis revealed that (1) a variety of social benefits are valued in studies that assess either of the four ecosystem service types, (2) certain social benefits are likely to co-occur in combination with certain cultural ecosystem services, (3) of the studies that employed monetary valuation techniques, simulated market approaches overlapped most frequently with the assessment of social benefits and (4) studies that directly incorporate stakeholder's views were more likely to also assess social benefits. (C) 2016 Elsevier B.V. All rights reserved.
Robust appraisals of climate impacts at different levels of global-mean temperature increase are vital to guide assessments of dangerous anthropogenic interference with the climate system. The 2015 Paris Agreement includes a two-headed temperature goal: "holding the increase in the global average temperature to well below 2 degrees C above pre-industrial levels and pursuing efforts to limit the temperature increase to 1.5 degrees C". Despite the prominence of these two temperature limits, a comprehensive overview of the differences in climate impacts at these levels is still missing. Here we provide an assessment of key impacts of climate change at warming levels of 1.5 degrees C and 2 degrees C, including extreme weather events, water availability, agricultural yields, sea-level rise and risk of coral reef loss. Our results reveal substantial differences in impacts between a 1.5 degrees C and 2 degrees C warming that are highly relevant for the assessment of dangerous anthropogenic interference with the climate system. For heat-related extremes, the additional 0.5 degrees C increase in global-mean temperature marks the difference between events at the upper limit of present-day natural variability and a new climate regime, particularly in tropical regions. Similarly, this warming difference is likely to be decisive for the future of tropical coral reefs. In a scenario with an end-of-century warming of 2 degrees C, virtually all tropical coral reefs are projected to be at risk of severe degradation due to temperature-induced bleaching from 2050 onwards. This fraction is reduced to about 90% in 2050 and projected to decline to 70% by 2100 for a 1.5 degrees C scenario. Analyses of precipitation-related impacts reveal distinct regional differences and hot-spots of change emerge. Regional reduction in median water availability for the Mediterranean is found to nearly double from 9% to 17% between 1.5 degrees C and 2 degrees C, and the projected lengthening of regional dry spells increases from 7 to 11%. Projections for agricultural yields differ between crop types as well as world regions. While some (in particular high-latitude) regions may benefit, tropical regions like West Africa, South-East Asia, as well as Central and northern South America are projected to face substantial local yield reductions, particularly for wheat and maize. Best estimate sea-level rise projections based on two illustrative scenarios indicate a 50cm rise by 2100 relative to year 2000-levels for a 2 degrees C scenario, and about 10 cm lower levels for a 1.5 degrees C scenario. In a 1.5 degrees C scenario, the rate of sea-level rise in 2100 would be reduced by about 30% compared to a 2 degrees C scenario. Our findings highlight the importance of regional differentiation to assess both future climate risks and different vulnerabilities to incremental increases in global-mean temperature. The article provides a consistent and comprehensive assessment of existing projections and a good basis for future work on refining our understanding of the difference between impacts at 1.5 degrees C and 2 degrees C warming.
The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [1, 2]. Specific pollinator attraction relies on visual and olfactory floral cues [3-5]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [6-8]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [9-13]. Benzenoids are an important class of floral scent compounds that are generated from phenylalanine via several enzymatic pathways [14-17]. Here we address the genetic basis of the loss of floral scent associated with the transition from outbreeding to selfing in the genus Capsella. While the outbreeding C. grandiflora emits benzaldehyde as a major constituent of its floral scent, this has been lost in the selfing C. rubella. We identify the Capsella CNL1 gene encoding cinnamate: CoA ligase as responsible for this variation. Population genetic analysis indicates that CNL1 has been inactivated twice independently in C. rubella via different novel mutations to its coding sequence. Together with a recent study in Petunia [18], this identifies cinnamate: CoA ligase as an evolutionary hotspot for mutations causing the loss of benzenoid scent compounds in association with a shift in the reproductive strategy of Capsella from pollination by insects to self-fertilization.
Background
Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)).
Methods
Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (β2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-β2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human β2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human β2GPI or after CL-micelle absorption.
Results
Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM aß2GPI and aCL. Anti-CL and anti-ß2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and ß2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized β2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-β2GPI humoAbs.
Conclusions
The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1.
More effort — more results
(2016)
The development of 'omics' technologies has progressed to address complex biological questions that underlie various plant functions thereby producing copious amounts of data. The need to assimilate large amounts of data into biologically meaningful interpretations has necessitated the development of statistical methods to integrate multidimensional information. Throughout this review, we provide examples of recent outcomes of 'omics' data integration together with an overview of available statistical methods and tools.
Background:
Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental
property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions
are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial
clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda
(insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate
the link between size and diversity within this ancient and highly diverse lineage.
Results:
The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally
distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions
typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a
negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these
two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within
Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution
within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes
including significant phylogenetic conservatism.
Conclusions:
Based on our findings we suggest that the use of models derived from well-studied but atypical clades,
such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results
indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect
diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large
timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available
data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may
collectively enhance our understanding of this key component of terrestrial ecosystems.
Arctic coastal infrastructure and cultural and archeological sites are increasingly vulnerable to erosion and flooding due to amplified warming of the Arctic, sea level rise, lengthening of open water periods, and a predicted increase in frequency of major storms. Mitigating these hazards necessitates decision-making tools at an appropriate scale. The objectives of this paper are to provide such a tool by assessing potential erosion and flood hazards at Herschel Island, a UNESCO World Heritage candidate site. This study focused on Simpson Point and the adjacent coastal sections because of their archeological, historical, and cultural significance. Shoreline movement was analyzed using the Digital Shoreline Analysis System (DSAS) after digitizing shorelines from 1952, 1970, 2000, and 2011. For purposes of this analysis, the coast was divided in seven coastal reaches (CRs) reflecting different morphologies and/or exposures. Using linear regression rates obtained from these data, projections of shoreline position were made for 20 and 50 years into the future. Flood hazard was assessed using a least cost path analysis based on a high-resolution light detection and ranging (LiDAR) dataset and current Intergovernmental Panel on Climate Change sea level estimates. Widespread erosion characterizes the study area. The rate of shoreline movement in different periods of the study ranges from −5.5 to 2.7 m·a⁻¹ (mean −0.6 m·a⁻¹). Mean coastal retreat decreased from −0.6 m·a⁻¹ to −0.5 m·a⁻¹, for 1952–1970 and 1970–2000, respectively, and increased to −1.3 m·a⁻¹ in the period 2000–2011. Ice-rich coastal sections most exposed to wave attack exhibited the highest rates of coastal retreat. The geohazard map combines shoreline projections and flood hazard analyses to show that most of the spit area has extreme or very high flood hazard potential, and some buildings are vulnerable to coastal erosion. This study demonstrates that transgressive forcing may provide ample sediment for the expansion of depositional landforms, while growing more susceptible to overwash and flooding.
Most climate change impacts manifest in the form of natural hazards. Damage assessment typically relies on damage functions that translate the magnitude of extreme events to a quantifiable damage. In practice, the availability of damage functions is limited due to a lack of data sources and a lack of understanding of damage processes. The study of the characteristics of damage functions for different hazards could strengthen the theoretical foundation of damage functions and support their development and validation. Accordingly, we investigate analogies of damage functions for coastal flooding and for wind storms and identify a unified approach. This approach has general applicability for granular portfolios and may also be applied, for example, to heat-related mortality. Moreover, the unification enables the transfer of methodology between hazards and a consistent treatment of uncertainty. This is demonstrated by a sensitivity analysis on the basis of two simple case studies (for coastal flood and storm damage). The analysis reveals the relevance of the various uncertainty sources at varying hazard magnitude and on both the microscale and the macroscale level. Main findings are the dominance of uncertainty from the hazard magnitude and the persistent behaviour of intrinsic uncertainties on both scale levels. Our results shed light on the general role of uncertainties and provide useful insight for the application of the unified approach.
Background
Dietary calcium (Ca) concentrations might affect regulatory pathways within the Ca and vitamin D metabolism and consequently excretory mechanisms. Considering large variations in Ca concentrations of feline diets, the physiological impact on Ca homeostasis has not been evaluated to date. In the present study, diets with increasing concentrations of dicalcium phosphate were offered to ten healthy adult cats (Ca/phosphorus (P): 6.23/6.02, 7.77/7.56, 15.0/12.7, 19.0/17.3, 22.2/19.9, 24.3/21.6 g/kg dry matter). Each feeding period was divided into a 10-day adaptation and an 8-day sampling period in order to collect urine and faeces. On the last day of each feeding period, blood samples were taken.
Results
Urinary Ca concentrations remained unaffected, but faecal Ca concentrations increased (P < 0.001) with increasing dietary Ca levels. No effect on whole and intact parathyroid hormone levels, fibroblast growth factor 23 and calcitriol concentrations in the blood of the cats were observed. However, the calcitriol precursors 25(OH)D-2 and 25(OH)D-3, which are considered the most useful indicators for the vitamin D status, decreased with higher dietary Ca levels (P = 0.013 and P = 0.033). Increasing dietary levels of dicalcium phosphate revealed an acidifying effect on urinary fasting pH (6.02) and postprandial pH (6.01) (P < 0.001), possibly mediated by an increase of urinary phosphorus (P) concentrations (P < 0.001).
Conclusions
In conclusion, calcitriol precursors were linearly affected by increasing dietary Ca concentrations. The increase in faecal Ca excretion indicates that Ca homeostasis of cats is mainly regulated in the intestine and not by the kidneys. Long-term studies should investigate the physiological relevance of the acidifying effect observed when feeding diets high in Ca and P.
Many previous studies have shown that the turbulent mixing layer under periodic forcing tends to adopt a lock-on state, where the major portion of the fluctuations in the flow are synchronized at the forcing frequency. The goal of this experimental study is to apply closed-loop control in order to provoke the lock-on state, using information from the flow itself. We aim to determine the range of frequencies for which the closed-loop control can establish the lock-on, and what mechanisms are contributing to the selection of a feedback frequency. In order to expand the solution space for optimal closed-loop control laws, we use the genetic programming control (CPC) framework. The best closed-loop control laws obtained by CPC are analysed along with the associated physical mechanisms in the mixing layer flow. The resulting closed-loop control significantly outperforms open-loop forcing in terms of robustness to changes in the free-stream velocities. In addition, the selection of feedback frequencies is not locked to the most amplified local mode, but rather a range of frequencies around it.
Exosomes are small membrane vesicles released by different cell types, including hepatocytes, that play important roles in intercellular communication. We have previously demonstrated that hepatocyte-derived exosomes contain the synthetic machinery to form sphingosine-1-phosphate (S1P) in target hepatocytes resulting in proliferation and liver regeneration after ischemia/reperfusion (I/R) injury. We also demonstrated that the chemokine receptors, CXCR1 and CXCR2, regulate liver recovery and regeneration after I/R injury. In the current study, we sought to determine if the regulatory effects of CXCR1 and CXCR2 on liver recovery and regeneration might occur via altered release of hepatocyte exosomes. We found that hepatocyte release of exosomes was dependent upon CXCR1 and CXCR2. CXCR1-deficient hepatocytes produced fewer exosomes, whereas CXCR2-deficient hepatocytes produced more exosomes compared to their wild-type controls. In CXCR2-deficient hepatocytes, there was increased activity of neutral sphingomyelinase (Nsm) and intracellular ceramide. CXCR1-deficient hepatocytes had no alterations in Nsm activity or ceramide production. Interestingly, exosomes from CXCR1-deficient hepatocytes had no effect on hepatocyte proliferation, due to a lack of neutral ceramidase and sphingosine kinase. The data demonstrate that CXCR1 and CXCR2 regulate hepatocyte exosome release. The mechanism utilized by CXCR1 remains elusive, but CXCR2 appears to modulate Nsm activity and resultant production of ceramide to control exosome release. CXCR1 is required for packaging of enzymes into exosomes that mediate their hepatocyte proliferative effect.
In the study of relativistic jets one of the key open questions is their interaction with the environment on the microscopic level. Here, we study the initial evolution of both electron-proton (e(-)-p(+)) and electron-positron (e(+/-)) relativistic jets containing helical magnetic fields, focusing on their interaction with an ambient plasma. We have performed simulations of "global" jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability (kKHI) and the Mushroom instability (MI). In our initial simulation study these kinetic instabilities are suppressed and new types of instabilities can grow. In the e(-)-p(+) jet simulation a recollimation-like instability occurs and jet electrons are strongly perturbed. In the e(+/-) jet simulation a recollimation-like instability occurs at early times followed by a kinetic instability and the general structure is similar to a simulation without helical magnetic field. Simulations using much larger systems are required in order to thoroughly follow the evolution of global jets containing helical magnetic fields.
The new sediment record from the deep Dead Sea basin (ICDP core 5017-1) provides a unique archive for hydroclimatic variability in the Levant. Here, we present high-resolution sediment facies analysis and elemental composition by micro-X-ray fluorescence (mu XRF) scanning of core 5017-1 to trace lake levels and responses of the regional hydroclimatology during the time interval from ca. 117 to 75 ka, i. e. the transition between the last interglacial and the onset of the last glaciation. We distinguished six major micro-facies types and interpreted these and their alterations in the core in terms of relative lake level changes. The two end-member facies for highest and lowest lake levels are (a) up to several metres thick, greenish sediments of alternating aragonite and detrital marl laminae (aad) and (b) thick halite facies, respectively. Intermediate lake levels are characterised by detrital marls with varying amounts of aragonite, gypsum or halite, reflecting lower-amplitude, shorter-term variability. Two intervals of pronounced lake level drops occurred at similar to 110-108 +/- 5 and similar to 93-87 +/- 7 ka. They likely coincide with stadial conditions in the central Mediterranean (Melisey I and II pollen zones in Monticchio) and low global sea levels during Marine Isotope Stage (MIS) 5d and 5b. However, our data do not support the current hypothesis of an almost complete desiccation of the Dead Sea during the earlier of these lake level low stands based on a recovered gravel layer. Based on new petrographic analyses, we propose that, although it was a low stand, this well-sorted gravel layer may be a vestige of a thick turbidite that has been washed out during drilling rather than an in situ beach deposit. Two intervals of higher lake stands at similar to 108-93 +/- 6 and similar to 87-75 +/- 7 ka correspond to interstadial conditions in the central Mediterranean, i. e. pollen zones St. Germain I and II in Monticchio, and Greenland interstadials (GI) 24+23 and 21 in Greenland, as well as to sapropels S4 and S3 in the Mediterranean Sea. These apparent correlations suggest a close link of the climate in the Levant to North Atlantic and Mediterranean climates during the time of the build-up of Northern Hemisphere ice shields in the early last glacial period.
Studies investigating the effect of increasing CO2 levels on the phosphorus cycle in natural waters are lacking although phosphorus often controls phytoplankton development in many aquatic systems. The aim of our study was to analyse effects of elevated CO2 levels on phosphorus pool sizes and uptake. The phosphorus dynamic was followed in a CO2-manipulation mesocosm experiment in the Storfjarden (western Gulf of Finland, Baltic Sea) in summer 2012 and was also studied in the surrounding fjord water. In all mesocosms as well as in surface waters of Storfjarden, dissolved organic phosphorus (DOP) concentrations of 0.26aEuro-+/- aEuro-0.03 and 0.23aEuro-+/- aEuro-0.04aEuro-A mu molaEuro-L-1, respectively, formed the main fraction of the total P-pool (TP), whereas phosphate (PO4) constituted the lowest fraction with mean concentration of 0.15aEuro-A +/- aEuro-0.02 in the mesocosms and 0.17aEuro-A +/- aEuro-0.07aEuro-A mu molaEuro-L-1 in the fjord. Transformation of PO4 into DOP appeared to be the main pathway of PO4 turnover. About 82aEuro-% of PO4 was converted into DOP whereby only 18aEuro-% of PO4 was transformed into particulate phosphorus (PP). PO4 uptake rates measured in the mesocosms ranged between 0.6 and 3.9aEuro-nmolaEuro-L(-1)aEuro-h(-1). About 86aEuro-% of them was realized by the size fraction < aEuro-3aEuro-A mu m. Adenosine triphosphate (ATP) uptake revealed that additional P was supplied from organic compounds accounting for 25-27aEuro-% of P provided by PO4 only. CO2 additions did not cause significant changes in phosphorus (P) pool sizes, DOP composition, and uptake of PO4 and ATP when the whole study period was taken into account. However, significant short-term effects were observed for PO4 and PP pool sizes in CO2 treatments > aEuro-1000aEuro-A mu atm during periods when phytoplankton biomass increased. In addition, we found significant relationships (e.g., between PP and Chl a) in the untreated mesocosms which were not observed under high fCO(2) conditions. Consequently, it can be hypothesized that the relationship between PP formation and phytoplankton growth changed with CO2 elevation. It can be deduced from the results, that visible effects of CO2 on P pools are coupled to phytoplankton growth when the transformation of PO4 into POP was stimulated. The transformation of PO4 into DOP on the other hand does not seem to be affected. Additionally, there were some indications that cellular mechanisms of P regulation might be modified under CO2 elevation changing the relationship between cellular constituents.
Turbidity measurements are frequently implemented for the monitoring of heterogeneous chemical, physical, or biotechnological processes. However, for quantitative measurements, turbidity probes need calibration, as is requested and regulated by the ISO 7027:1999. Accordingly, a formazine suspension has to be produced. Despite this regulatory demand, no scientific publication on the stability and reproducibility of this polymerization process is available. In addition, no characterization of the optical properties of this calibration material with other optical methods had been achieved so far. Thus, in this contribution, process conditions such as temperature and concentration have been systematically investigated by turbidity probe measurements and Photon Density Wave (PDW) spectroscopy, revealing an influence on the temporal formazine formation onset. In contrast, different reaction temperatures do not lead to different scattering properties for the final formazine suspensions, but give an access to the activation energy for this condensation reaction. Based on PDW spectroscopy data, the synthesis of formazine is reproducible. However, very strong influences of the ambient conditions on the measurements of the turbidity probe have been observed, limiting its applicability. The restrictions of the turbidity probe with respect to scatterer concentration are examined on the basis of formazine and polystyrene suspensions. Compared to PDW spectroscopy data, signal saturation is observed at already low reduced scattering coefficients.
In low-accumulation regions, the reliability of delta O-18-derived temperature signals from ice cores within the Holocene is unclear, primarily due to the small climate changes relative to the intrinsic noise of the isotopic signal. In order to learn about the representativity of single ice cores and to optimise future ice-core-based climate reconstructions, we studied the stable-water isotope composition of firn at Kohnen Station, Dronning Maud Land, Antarctica. Analysing delta O-18 in two 50m long snow trenches allowed us to create an unprecedented, two-dimensional image characterising the isotopic variations from the centimetre to the 100-metre scale. Our results show seasonal layering of the isotopic composition but also high horizontal isotopic variability caused by local stratigraphic noise. Based on the horizontal and vertical structure of the isotopic variations, we derive a statistical noise model which successfully explains the trench data. The model further allows one to determine an upper bound for the reliability of climate reconstructions conducted in our study region at seasonal to annual resolution, depending on the number and the spacing of the cores taken.
We present a summary on the current status of two inversion algorithms that are used in EARLINET (European Aerosol Research Lidar Network) for the inversion of data collected with EARLINET multiwavelength Raman lidars. These instruments measure backscatter coefficients at 355, 532, and 1064 nm, and extinction coefficients at 355 and 532 nm. Development of these two algorithms started in 2000 when EARLINET was founded. The algorithms are based on a manually controlled inversion of optical data which allows for detailed sensitivity studies. The algorithms allow us to derive particle effective radius as well as volume and surface area concentration with comparably high confidence. The retrieval of the real and imaginary parts of the complex refractive index still is a challenge in view of the accuracy required for these parameters in climate change studies in which light absorption needs to be known with high accuracy. It is an extreme challenge to retrieve the real part with an accuracy better than 0.05 and the imaginary part with accuracy better than 0.005-0.1 or +/- 50 %. Single-scattering albedo can be computed from the retrieved microphysical parameters and allows us to categorize aerosols into high-and low-absorbing aerosols.
On the basis of a few exemplary simulations with synthetic optical data we discuss the current status of these manually operated algorithms, the potentially achievable accuracy of data products, and the goals for future work. One algorithm was used with the purpose of testing how well microphysical parameters can be derived if the real part of the complex refractive index is known to at least 0.05 or 0.1. The other algorithm was used to find out how well microphysical parameters can be derived if this constraint for the real part is not applied.
The optical data used in our study cover a range of Angstrom exponents and extinction-to-backscatter (lidar) ratios that are found from lidar measurements of various aerosol types. We also tested aerosol scenarios that are considered highly unlikely, e.g. the lidar ratios fall outside the commonly accepted range of values measured with Raman lidar, even though the underlying microphysical particle properties are not uncommon. The goal of this part of the study is to test the robustness of the algorithms towards their ability to identify aerosol types that have not been measured so far, but cannot be ruled out based on our current knowledge of aerosol physics.
We computed the optical data from monomodal logarithmic particle size distributions, i.e. we explicitly excluded the more complicated case of bimodal particle size distributions which is a topic of ongoing research work. Another constraint is that we only considered particles of spherical shape in our simulations. We considered particle radii as large as 7-10 mu m in our simulations where the Potsdam algorithm is limited to the lower value. We considered optical-data errors of 15% in the simulation studies. We target 50% uncertainty as a reasonable threshold for our data products, though we attempt to obtain data products with less uncertainty in future work.
We analyzed the population genetic pattern of 12 fragmented Geropogon hybridus ecological range edge populations in Israel along a steep precipitation gradient. In the investigation area (45 x 20 km(2)), the annual mean precipitation changes rapidly from 450 mm in the north (Mediterranean-influenced climate zone) to 300 mm in the south (semiarid climate zone) without significant temperature changes. Our analysis (91 individuals, 12 populations, 123 polymorphic loci) revealed strongly structured populations (AMOVA I broken vertical bar(ST) = 0.35; P < 0.001); however, differentiation did not change gradually toward range edge. IBD was significant (Mantel test r = 0.81; P = 0.001) and derived from sharply divided groups between the northernmost populations and the others further south, due to dispersal or environmental limitations. This was corroborated by the PCA and STRUCTURE analyses. IBD and IBE were significant despite the micro-geographic scale of the study area, which indicates that reduced precipitation toward range edge leads to population genetic divergence. However, this pattern diminished when the hypothesized gene flow barrier was taken into account. Applying the spatial analysis method revealed 11 outlier loci that were correlated to annual precipitation and, moreover, were indicative for putative precipitation-related adaptation (BAYESCAN, MCHEZA). The results suggest that even on micro-geographic scales, environmental factors play prominent roles in population divergence, genetic drift, and directional selection. The pattern is typical for strong environmental gradients, e.g., at species range edges and ecological limits, and if gene flow barriers and mosaic-like structures of fragmented habitats hamper dispersal.
Brief communication
(2016)
In March 2015, a new international blueprint for disaster risk reduction (DRR) was adopted in Sendai, Japan, at the end of the Third UN World Conference on Disaster Risk Reduction (WCDRR, 14-18 March 2015). We review and discuss the agreed commitments and targets, as well as the negotiation leading the Sendai Framework for DRR (SF-DRR) and discuss briefly its implication for the later UN-led negotiations on sustainable development goals and climate change.
To understand past flood changes in the Rhine catchment and in particular the role of anthropogenic climate change in extreme flows, an attribution study relying on a proper GCM (general circulation model) downscaling is needed. A downscaling based on conditioning a stochastic weather generator on weather patterns is a promising approach. This approach assumes a strong link between weather patterns and local climate, and sufficient GCM skill in reproducing weather pattern climatology. These presuppositions are unprecedentedly evaluated here using 111 years of daily climate data from 490 stations in the Rhine basin and comprehensively testing the number of classification parameters and GCM weather pattern characteristics. A classification based on a combination of mean sea level pressure, temperature, and humidity from the ERA20C reanalysis of atmospheric fields over central Europe with 40 weather types was found to be the most appropriate for stratifying six local climate variables. The corresponding skill is quite diverse though, ranging from good for radiation to poor for precipitation. Especially for the latter it was apparent that pressure fields alone cannot sufficiently stratify local variability. To test the skill of the latest generation of GCMs from the CMIP5 ensemble in reproducing the frequency, seasonality, and persistence of the derived weather patterns, output from 15 GCMs is evaluated. Most GCMs are able to capture these characteristics well, but some models showed consistent deviations in all three evaluation criteria and should be excluded from further attribution analysis.
Antibodies against spike proteins of influenza are used as a tool for characterization of viruses and therapeutic approaches. However, development, production and quality control of antibodies is expensive and time consuming. To circumvent these difficulties, three peptides were derived from complementarity determining regions of an antibody heavy chain against influenza A spike glycoprotein. Their binding properties were studied experimentally, and by molecular dynamics simulations. Two peptide candidates showed binding to influenza A/Aichi/2/68 H3N2. One of them, termed PeB, with the highest affinity prevented binding to and infection of target cells in the micromolar region without any cytotoxic effect. PeB matches best the conserved receptor binding site of hemagglutinin. PeB bound also to other medical relevant influenza strains, such as human-pathogenic A/California/7/2009 H1N1, and avian-pathogenic A/MuteSwan/Rostock/R901/2006 H7N1. Strategies to improve the affinity and to adapt specificity are discussed and exemplified by a double amino acid substituted peptide, obtained by substitutional analysis. The peptides and their derivatives are of great potential for drug development as well as biosensing.
The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity.
Relatedness strongly influences social behaviors in a wide variety of species. For most species, the highest typical degree of relatedness is between full siblings with 50% shared genes. However, this is poorly understood in species with unusually high relatedness between individuals: clonal organisms. Although there has been some investigation into clonal invertebrates and yeast, nothing is known about kin selection in clonal vertebrates. We show that a clonal fish, the Amazon molly (Poecilia formosa), can distinguish between different clonal lineages, associating with genetically identical, sister clones, and use multiple sensory modalities. Also, they scale their aggressive behaviors according to the relatedness to other females: they are more aggressive to non-related clones. Our results demonstrate that even in species with very small genetic differences between individuals, kin recognition can be adaptive. Their discriminatory abilities and regulation of costly behaviors provides a powerful example of natural selection in species with limited genetic diversity.
Background:
Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize
survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different
levels of gene expression.
Results:
Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of
Arabidopsis thaliana
to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is
modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of
genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are
likely candidates to play a role in regulating translation of those genes.
Conclusions:
Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids
is maintained upon heat exposure.
The onset of modern central Asian atmospheric circulation is traditionally linked to the interplay of surface uplift of the Mongolian and Tibetan-Himalayan orogens, retreat of the Paratethys sea from central Asia and Cenozoic global cooling. Although the role of these players has not yet been unravelled, the vast dust deposits of central China support the presence of arid conditions and modern atmospheric pathways for the last 25 million years (Myr). Here, we present provenance data from older (42-33 Myr) dust deposits, at a time when the Tibetan Plateau was less developed, the Paratethys sea still present in central Asia and atmospheric pCO(2) much higher. Our results show that dust sources and near-surface atmospheric circulation have changed little since at least 42 Myr. Our findings indicate that the locus of central Asian high pressures and concurrent aridity is a resilient feature only modulated by mountain building, global cooling and sea retreat.
Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.
In recent decades, the Greenland Ice Sheet has been losing mass and has thereby contributed to global sea-level rise. The rate of ice loss is highly relevant for coastal protection worldwide. The ice loss is likely to increase under future warming. Beyond a critical temperature threshold, a meltdown of the Greenland Ice Sheet is induced by the self-enforcing feedback between its lowering surface elevation and its increasing surface mass loss: the more ice that is lost, the lower the ice surface and the warmer the surface air temperature, which fosters further melting and ice loss. The computation of this rate so far relies on complex numerical models which are the appropriate tools for capturing the complexity of the problem. By contrast we aim here at gaining a conceptual understanding by deriving a purposefully simple equation for the self-enforcing feedback which is then used to estimate the melt time for different levels of warming using three observable characteristics of the ice sheet itself and its surroundings. The analysis is purely conceptual in nature. It is missing important processes like ice dynamics for it to be useful for applications to sea-level rise on centennial timescales, but if the volume loss is dominated by the feedback, the resulting logarithmic equation unifies existing numerical simulations and shows that the melt time depends strongly on the level of warming with a critical slow-down near the threshold: the median time to lose 10% of the present-day ice volume varies between about 3500 years for a temperature level of 0.5 degrees C above the threshold and 500 years for 5 degrees C. Unless future observations show a significantly higher melting sensitivity than currently observed, a complete meltdown is unlikely within the next 2000 years without significant ice-dynamical contributions.