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Subsurface lateral flow in hillslope soils depends on lower permeability or texture-contrasting soil horizons. In the arable hummocky soil landscape, erosion processes caused glacial till appearance closer to the soil surface at upslope positions. The objective of this work was to quantify the potential for subsurface lateral flow depending on the erosion-affected spatial hydropedological complexity. The eroded Haplic Luvisol profile was studied due to the presence of a relatively dense C horizon that varied in depth, thickness, and sloping angle. A two-dimensional numerical modeling and sensitivity analysis for the saturated hydraulic conductivity (K-s) of the C horizon and the depth to C horizon (i.e., soil solum thickness) was performed for rainstorms in 2011 and 2012 using HYDRUS-2D. A K-s value of <2.5 cm d(-1) for the C horizon was required for lateral flow initiation. Lateral flow was (i) increasing with decreasing solum thickness, indicating an erosion-induced feedback on subsurface lateral flow, and (ii) dependent on the soil moisture regime prior to rainstorms. The effect of lateral flow on the movement of a conservative tracer was simulated in the form of a "virtual experiment". Simulation scenarios revealed only a relatively small lateral shift of the tracer plume caused by a local decoupling of water (already lateral) from subsequent tracer movement (still vertical). Longer term simulations suggested that, for the present conditions, lateral flow was limited mostly to occasional summer storm events. Even without considering preferential flow contribution to lateral flow, highly complex hydropedologic interactions are present in erosion-affected heterogeneous soil profiles.
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data. From a methodological point, we show that the coupling of tissue-specific models in a multi-tissue model yields a higher specificity of the interconnected models with respect to network structure and flux distributions. We use the extracted models to predict and investigate the flux of the growth hormone indole-3-actetate and its antagonist, trans-Zeatin, through the root. While some of predictions are in line with experimental evidence, constraints other than those coming from the metabolic level may be necessary to replicate the flow of indole-3-actetate from other simulation studies. Therefore, our work provides the means for data-driven multi-tissue metabolic model extraction of other Arabidopsis organs in the constraint-based modeling framework.
The synthetic yeast genome constructed by the International Synthetic Yeast Sc2.0 consortium adds thousands of loxPsym recombination sites to all 16 redesigned chromosomes, allowing the shuffling of Sc2.0 chromosome parts by the Cre-loxP recombination system thereby enabling genome evolution experiments. Here, we present L-SCRaMbLE, a lightcontrolled Cre recombinase for use in the yeast Saccharomyces cerevisiae. L-SCRaMbLE allows tight regulation of recombinase activity with up to 179-fold induction upon exposure to red light. The extent of recombination depends on induction time and concentration of the chromophore phycocyanobilin (PCB), which can be easily adjusted. The tool presented here provides improved recombination control over the previously reported estradiol-dependent SCRaMbLE induction system, mediating a larger variety of possible recombination events in SCRaMbLE-ing a reporter plasmid. Thereby, L-SCRaMbLE boosts the potential for further customization and provides a facile application for use in the S. cerevisiae genome reengineering project Sc2.0 or in other recombination-based systems.
The fact that organic solar cells perform efficiently despite the low dielectric constant of most photoactive blends initiated a long-standing debate regarding the dominant pathways of free charge formation. Here, we address this issue through the accurate measurement of the activation energy for free charge photogeneration over a wide range of photon energy, using the method of time-delayed collection field. For our prototypical low bandgap polymer:fullerene blends, we find that neither the temperature nor the field dependence of free charge generation depend on the excitation energy, ruling out an appreciable contribution to free charge generation though hot carrier pathways. On the other hand, activation energies are on the order of the room temperature thermal energy for all studied blends. We conclude that charge generation in such devices proceeds through thermalized charge transfer states, and that thermal energy is sufficient to separate most of these states into free charges.
The oldest ice core records are obtained from the East Antarctic Plateau. Water isotopes are key proxies to reconstructing past climatic conditions over the ice sheet and at the evaporation source. The accuracy of climate reconstructions depends on knowledge of all processes affecting water vapour, precipitation and snow isotopic compositions. Fractionation processes are well understood and can be integrated in trajectory-based Rayleigh distillation and isotope-enabled climate models. However, a quantitative understanding of processes potentially altering snow isotopic composition after deposition is still missing. In low-accumulation sites, such as those found in East Antarctica, these poorly constrained processes are likely to play a significant role and limit the interpretability of an ice core's isotopic composition.
By combining observations of isotopic composition in vapour, precipitation, surface snow and buried snow from Dome C, a deep ice core site on the East Antarctic Plateau, we found indications of a seasonal impact of metamorphism on the surface snow isotopic signal when compared to the initial precipitation. Particularly in summer, exchanges of water molecules between vapour and snow are driven by the diurnal sublimation-condensation cycles. Overall, we observe in between precipitation events modification of the surface snow isotopic composition. Using high-resolution water isotopic composition profiles from snow pits at five Antarctic sites with different accumulation rates, we identified common patterns which cannot be attributed to the seasonal variability of precipitation. These differences in the precipitation, surface snow and buried snow isotopic composition provide evidence of post-deposition processes affecting ice core records in low-accumulation areas.
Most large-scale hydrologic models fall short in reproducing groundwater head dynamics and simulating transport process due to their oversimplified representation of groundwater flow. In this study, we aim to extend the applicability of the mesoscale Hydrologic Model (mHM v5.7) to subsurface hydrology by coupling it with the porous media simulator OpenGeoSys (OGS). The two models are one-way coupled through model interfaces GIS2FEM and RIV2FEM, by which the grid-based fluxes of groundwater recharge and the river-groundwater exchange generated by mHM are converted to fixed-flux boundary conditions of the groundwater model OGS. Specifically, the grid-based vertical reservoirs in mHM are completely preserved for the estimation of land-surface fluxes, while OGS acts as a plug-in to the original mHM modeling framework for groundwater flow and transport modeling. The applicability of the coupled model (mHM-OGS v1.0) is evaluated by a case study in the central European mesoscale river basin - Nagelstedt. Different time steps, i.e., daily in mHM and monthly in OGS, are used to account for fast surface flow and slow groundwater flow. Model calibration is conducted following a two-step procedure using discharge for mHM and long-term mean of groundwater head measurements for OGS. Based on the model summary statistics, namely the Nash-Sutcliffe model efficiency (NSE), the mean absolute error (MAE), and the interquartile range error (QRE), the coupled model is able to satisfactorily represent the dynamics of discharge and groundwater heads at several locations across the study basin. Our exemplary calculations show that the one-way coupled model can take advantage of the spatially explicit modeling capabilities of surface and groundwater hydrologic models and provide an adequate representation of the spatiotemporal behaviors of groundwater storage and heads, thus making it a valuable tool for addressing water resources and management problems.
Ecoevolutionary feedbacks in predator-prey systems have been shown to qualitatively alter predator-prey dynamics. As a striking example, defense-offense coevolution can reverse predator-prey cycles, so predator peaks precede prey peaks rather than vice versa. However, this has only rarely been shown in either model studies or empirical systems. Here, we investigate whether this rarity is a fundamental feature of reversed cycles by exploring under which conditions they should be found. For this, we first identify potential conditions and parameter ranges most likely to result in reversed cycles by developing a new measure, the effective prey biomass, which combines prey biomass with prey and predator traits, and represents the prey biomass as perceived by the predator. We show that predator dynamics always follow the dynamics of the effective prey biomass with a classic 1/4-phase lag. From this key insight, it follows that in reversed cycles (i.e., -lag), the dynamics of the actual and the effective prey biomass must be in antiphase with each other, that is, the effective prey biomass must be highest when actual prey biomass is lowest, and vice versa. Based on this, we predict that reversed cycles should be found mainly when oscillations in actual prey biomass are small and thus have limited impact on the dynamics of the effective prey biomass, which are mainly driven by trait changes. We then confirm this prediction using numerical simulations of a coevolutionary predator-prey system, varying the amplitude of the oscillations in prey biomass: Reversed cycles are consistently associated with regions of parameter space leading to small-amplitude prey oscillations, offering a specific and highly testable prediction for conditions under which reversed cycles should occur in natural systems.
The hydrolytic stability of polymers to be used for coatings in aqueous environments, for example, to confer anti-fouling properties, is crucial. However, long-term exposure studies on such polymers are virtually missing. In this context, we synthesized a set of nine polymers that are typically used for low-fouling coatings, comprising the well-established poly(oligoethylene glycol methylether methacrylate), poly(3-(N-2-methacryloylethyl-N,N-dimethyl) ammoniopropanesulfonate) (sulfobetaine methacrylate), and poly(3-(N-3-methacryamidopropyl-N,N-dimethyl)ammoniopropanesulfonate) (sulfobetaine methacrylamide) as well as a series of hitherto rarely studied polysulfabetaines, which had been suggested to be particularly hydrolysis-stable. Hydrolysis resistance upon extended storage in aqueous solution is followed by H-1 NMR at ambient temperature in various pH regimes. Whereas the monomers suffered slow (in PBS) to very fast hydrolysis (in 1 M NaOH), the polymers, including the polymethacrylates, proved to be highly stable. No degradation of the carboxyl ester or amide was observed after one year in PBS, 1 M HCl, or in sodium carbonate buffer of pH 10. This demonstrates their basic suitability for anti-fouling applications. Poly(sulfobetaine methacrylamide) proved even to be stable for one year in 1 M NaOH without any signs of degradation. The stability is ascribed to a steric shielding effect. The hemisulfate group in the polysulfabetaines, however, was found to be partially labile.
Cell-free protein synthesis as a novel tool for directed glycoengineering of active erythropoietin
(2018)
As one of the most complex post-translational modification, glycosylation is widely involved in cell adhesion, cell proliferation and immune response. Nevertheless glycoproteins with an identical polypeptide backbone mostly differ in their glycosylation patterns. Due to this heterogeneity, the mapping of different glycosylation patterns to their associated function is nearly impossible. In the last years, glycoengineering tools including cell line engineering, chemoenzymatic remodeling and site-specific glycosylation have attracted increasing interest. The therapeutic hormone erythropoietin (EPO) has been investigated in particular by various groups to establish a production process resulting in a defined glycosylation pattern. However commercially available recombinant human EPO shows batch-to-batch variations in its glycoforms. Therefore we present an alternative method for the synthesis of active glycosylated EPO with an engineered O-glycosylation site by combining eukaryotic cell-free protein synthesis and site-directed incorporation of non-canonical amino acids with subsequent chemoselective modifications.
Ocean-induced melting below ice shelves is one of the dominant drivers for mass loss from the Antarctic Ice Sheet at present. An appropriate representation of sub-shelf melt rates is therefore essential for model simulations of marine-based ice sheet evolution. Continental-scale ice sheet models often rely on simple melt-parameterizations, in particular for long-term simulations, when fully coupled ice-ocean interaction becomes computationally too expensive. Such parameterizations can account for the influence of the local depth of the ice-shelf draft or its slope on melting. However, they do not capture the effect of ocean circulation underneath the ice shelf. Here we present the Potsdam Ice-shelf Cavity mOdel (PICO), which simulates the vertical overturning circulation in ice-shelf cavities and thus enables the computation of sub-shelf melt rates consistent with this circulation. PICO is based on an ocean box model that coarsely resolves ice shelf cavities and uses a boundary layer melt formulation. We implement it as a module of the Parallel Ice Sheet Model (PISM) and evaluate its performance under present-day conditions of the Southern Ocean. We identify a set of parameters that yield two-dimensional melt rate fields that qualitatively reproduce the typical pattern of comparably high melting near the grounding line and lower melting or refreezing towards the calving front. PICO captures the wide range of melt rates observed for Antarctic ice shelves, with an average of about 0.1 ma(-1) for cold sub-shelf cavities, for example, underneath Ross or Ronne ice shelves, to 16 ma(-1) for warm cavities such as in the Amundsen Sea region. This makes PICO a computationally feasible and more physical alternative to melt parameterizations purely based on ice draft geometry.