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- ItemDatasets from a vapor diffusion mineral precipitation protocol for Dictyostelium stalks(Amsterdam : Elsevier, 2016) Eder, Magdalena; Muth, Christina; Weiss, Ingrid M.Datasets from a slow carbonate vapor diffusion and mineral precipitation protocol for Dictyostelium ECM and cellulose stalks show examples for composite materials obtained by an in vitro approach, which differs substantially from the in vivo approach reported in The Journal of Structural Biology, doi: 10.1016/j.jsb.2016.03.015 [1]. Methods for obtaining the datasets include bright field transmitted light microscopy, fluorescence microscopy, LC-PolScope birefringence microscopy, variable pressure scanning electron microscopy (VP-SEM/ESEM), and Raman imaging spectroscopy.
- ItemGli protein activity is controlled by multisite phosphorylation in vertebrate hedgehog signaling(Amsterdam : Elsevier, 2013) Niewiadomski, Pawel; Kong, Jennifer H.; Ahrends, Robert; Ma, Yan; Humke, Eric W.; Khan, Sohini; Teruel, Mary N.; Novitch, Bennett G.; Rohatgi, RajatGli proteins are transcriptional effectors of the Hedgehog (Hh) pathway in both normal development and cancer. We describe a program of multisite phosphorylation that regulates the conversion of Gli proteins into transcriptional activators. In the absence of Hh ligands, Gli activity is restrained by the direct phosphorylation of six conserved serine residues by protein kinase A (PKA), a master negative regulator of the Hh pathway. Activation of signaling leads to a global remodeling of the Gli phosphorylation landscape: the PKA target sites become dephosphorylated, while a second cluster of sites undergoes phosphorylation. The pattern of Gli phosphorylation can regulate Gli transcriptional activity in a graded fashion, suggesting a phosphorylation-based mechanism for how a gradient of Hh signaling in a morphogenetic field can be converted into a gradient of transcriptional activity.
- ItemFossil-fueled development (SSP5): An energy and resource intensive scenario for the 21st century(Amsterdam : Elsevier, 2016) Kriegler, Elmar; Bauer, Nico; Popp, Alexander; Humpenöder, Florian; Leimbach, Marian; Strefler, Jessica; Baumstark, Lavinia; Bodirsky, Benjamin Leon; Hilaire, Jérôme; Klein, David; Mouratiadou, Ioanna; Weindl, Isabelle; Bertram, Christoph; Dietrich, Jan-Philipp; Luderer, Gunnar; Pehl, Michaja; Pietzcker, Robert; Piontek, Franziska; Lotze-Campen, Hermann; Biewald, Anne; Bonsch, Markus; Giannousakis, Anastasis; Kreidenweis, Ulrich; Müller, Christoph; Rolinski, Susanne; Schultes, Anselm; Schwanitz, Jana; Stevanovic, Miodrag; Calvin, Katherine; Emmerling, Johannes; Fujimori, Shinichiro; Edenhofer, OttmarThis paper presents a set of energy and resource intensive scenarios based on the concept of Shared Socio-Economic Pathways (SSPs). The scenario family is characterized by rapid and fossil-fueled development with high socio-economic challenges to mitigation and low socio-economic challenges to adaptation (SSP5). A special focus is placed on the SSP5 marker scenario developed by the REMIND-MAgPIE integrated assessment modeling framework. The SSP5 baseline scenarios exhibit very high levels of fossil fuel use, up to a doubling of global food demand, and up to a tripling of energy demand and greenhouse gas emissions over the course of the century, marking the upper end of the scenario literature in several dimensions. These scenarios are currently the only SSP scenarios that result in a radiative forcing pathway as high as the highest Representative Concentration Pathway (RCP8.5). This paper further investigates the direct impact of mitigation policies on the SSP5 energy, land and emissions dynamics confirming high socio-economic challenges to mitigation in SSP5. Nonetheless, mitigation policies reaching climate forcing levels as low as in the lowest Representative Concentration Pathway (RCP2.6) are accessible in SSP5. The SSP5 scenarios presented in this paper aim to provide useful reference points for future climate change, climate impact, adaption and mitigation analysis, and broader questions of sustainable development.
- ItemUncertainty in the measurement of indoor temperature and humidity in naturally ventilated dairy buildings as influenced by measurement technique and data variability(Amsterdam : Elsevier, 2017) Hempel, Sabrina; König, Marcel; Menz, Christoph; Janke, David; Amon, Barbara; Banhazi, Thomas M.; Estellés, Fernando; Amon, ThomasThe microclimatic conditions in dairy buildings affect animal welfare and gaseous emissions. Measurements are highly variable due to the inhomogeneous distribution of heat and humidity sources (related to farm management) and the turbulent inflow (associated with meteorologic boundary conditions). The selection of the measurement strategy (number and position of the sensors) and the analysis methodology adds to the uncertainty of the applied measurement technique. To assess the suitability of different sensor positions, in situations where monitoring in the direct vicinity of the animals is not possible, we collected long-term data in two naturally ventilated dairy barns in Germany between March 2015 and April 2016 (horizontal and vertical profiles with 10 to 5 min temporal resolution). Uncertainties related to the measurement setup were assessed by comparing the device outputs under lab conditions after the on-farm experiments. We found out that the uncertainty in measurements of relative humidity is of particular importance when assessing heat stress risk and resulting economic losses in terms of temperature-humidity index. Measurements at a height of approximately 3 m–3.5 m turned out to be a good approximation for the microclimatic conditions in the animal occupied zone (including the air volume close to the emission active zone). However, further investigation along this cross-section is required to reduce uncertainties related to the inhomogeneous distribution of humidity. In addition, a regular sound cleaning (and if possible recalibration after few months) of the measurement devices is crucial to reduce the instrumentation uncertainty in long-term monitoring of relative humidity in dairy barns. © 2017 The Authors
- ItemFuture growth patterns of world regions – A GDP scenario approach(Amsterdam : Elsevier, 2015) Leimbach, Marian; Kriegler, Elmar; Roming, Niklas; Schwanitz, JanaGlobal GDP projections for the 21st century are needed for the exploration of long-term global environmental problems, in particular climate change. Greenhouse gas emissions as well as climate change mitigation and adaption capacities strongly depend on growth of per capita income. However, long-term economic projections are highly uncertain. This paper provides five new long-term economic scenarios as part of the newly developed shared socio-economic pathways (SSPs) which represent a set of widely diverging narratives. A method of GDP scenario building is presented that is based on assumptions about technological progress, and human and physical capital formation as major drivers of long-term GDP per capita growth. The impact of these drivers differs significantly between different shared socio-economic pathways and is traced back to the underlying narratives and the associated population and education scenarios. In a highly fragmented world, technological and knowledge spillovers are low. Hence, the growth impact of technological progress and human capital is comparatively low, and per capita income diverges between world regions. These factors play a much larger role in globalization scenarios, leading to higher economic growth and stronger convergence between world regions. At the global average, per capita GDP is projected to grow annually in a range between 1.0% (SSP3) and 2.8% (SSP5) from 2010 to 2100. While this covers a large portion of variety in future global economic growth projections, plausible lower and higher growth projections may still be conceivable. The GDP projections are put into the context of historic patterns of economic growth (stylized facts), and their sensitivity to key assumptions is explored.
- ItemEnergy, land-use and greenhouse gas emissions trajectories under a green growth paradigm(Amsterdam : Elsevier, 2016) van Vuuren, Detlef P.; Stehfest, Elke; Gernaat, David E.H.J.; Doelman, Jonathan C.; van den Berg, Maarten; Harmsen, Mathijs; de Boer, Harmen Sytze; Bouwman, Lex F.; Daioglou, Vassilis; Edelenbosch, Oreane Y.; Girod, Bastien; Kram, Tom; Lassaletta, Luis; Lucas, Paul L.; van Meijl, Hans; Müller, Christoph; van Ruijven, Bas J.; van der Sluis, Sietske; Tabeau, AndrzejThis paper describes the possible developments in global energy use and production, land use, emissions and climate changes following the SSP1 storyline, a development consistent with the green growth (or sustainable development) paradigm (a more inclusive development respecting environmental boundaries). The results are based on the implementation using the IMAGE 3.0 integrated assessment model and are compared with a) other IMAGE implementations of the SSPs (SSP2 and SSP3) and b) the SSP1 implementation of other integrated assessment models. The results show that a combination of resource efficiency, preferences for sustainable production methods and investment in human development could lead to a strong transition towards a more renewable energy supply, less land use and lower anthropogenic greenhouse gas emissions in 2100 than in 2010, even in the absence of explicit climate policies. At the same time, climate policy would still be needed to reduce emissions further, in order to reduce the projected increase of global mean temperature from 3 °C (SSP1 reference scenario) to 2 or 1.5 °C (in line with current policy targets). The SSP1 storyline could be a basis for further discussions on how climate policy can be combined with achieving other societal goals.
- ItemChallenges in producing policy-relevant global scenarios of biodiversity and ecosystem services(Amsterdam : Elsevier, 2020) Rosa, Isabel M.D.; Purvis, Andy; Alkemade, Rob; Chaplin-Kramer, Rebecca; Ferrier, Simon; Guerra, Carlos A.; Hurtt, George; Kim, HyeJin; Leadley, Paul; Martins, Inês S.; Popp, Alexander; Schipper, Aafke M.; van Vuuren, Detlef; Pereira, Henrique M.Scenario-based modelling is a powerful tool to describe relationships between plausible trajectories of drivers, possible policy interventions, and impacts on biodiversity and ecosystem services. Model inter-comparisons are key in quantifying uncertainties and identifying avenues for model improvement but have been missing among the global biodiversity and ecosystem services modelling communities. The biodiversity and ecosystem services scenario-based inter-model comparison (BES-SIM) aims to fill this gap. We used global land-use and climate projections to simulate possible future impacts on terrestrial biodiversity and ecosystem services using a variety of models and a range of harmonized metrics. The goal of this paper is to reflect on the steps taken in BES-SIM, identify remaining methodological challenges, and suggest pathways for improvement. We identified five major groups of challenges; the need to: 1) better account for the role of nature in future human development storylines; 2) improve the representation of drivers in the scenarios by increasing the resolution (temporal, spatial and thematic) of land-use as key driver of biodiversity change and including additional relevant drivers; 3) explicitly integrate species- and trait-level biodiversity in ecosystem services models; 4) expand the coverage of the multiple dimensions of biodiversity and ecosystem services; and finally, 5) incorporate time-series or one-off historical data in the calibration and validation of biodiversity and ecosystem services models. Addressing these challenges would allow the development of more integrated global projections of biodiversity and ecosystem services, thereby improving their policy relevance in supporting the interlinked international conservation and sustainable development agendas. © 2019 The Authors
- ItemMembrane Tension Orchestrates Rear Retraction in Matrix-Directed Cell Migration(Amsterdam : Elsevier, 2019) Hetmanski, J.H.R.; de, Belly, H.; Busnelli, I.; Waring, T.; Nair, R.V.; Sokleva, V.; Dobre, O.; Cameron, A.; Gauthier, N.; Lamaze, C.; Swift, J.; del, Campo, A.; Starborg, T.; Zech, T.; Goetz, J.G.; Paluch, E.K.; Schwartz, J.-M.; Caswell, P.T.In development, wound healing, and cancer metastasis, vertebrate cells move through 3D interstitial matrix, responding to chemical and physical guidance cues. Protrusion at the cell front has been extensively studied, but the retraction phase of the migration cycle is not well understood. Here, we show that fast-moving cells guided by matrix cues establish positive feedback control of rear retraction by sensing membrane tension. We reveal a mechanism of rear retraction in 3D matrix and durotaxis controlled by caveolae, which form in response to low membrane tension at the cell rear. Caveolae activate RhoA-ROCK1/PKN2 signaling via the RhoA guanidine nucleotide exchange factor (GEF) Ect2 to control local F-actin organization and contractility in this subcellular region and promote translocation of the cell rear. A positive feedback loop between cytoskeletal signaling and membrane tension leads to rapid retraction to complete the migration cycle in fast-moving cells, providing directional memory to drive persistent cell migration in complex matrices. © 2019 The AuthorsCell migration through 3D matrix is critical to developmental and disease processes, but the mechanisms that control rear retraction are poorly understood. Hetmanski et al. show that differential membrane tension allows caveolae to form at the rear of migrating cells and activate the contractile actin cytoskeleton to promote rapid retraction. © 2019 The Authors
- ItemSurviving the surf: The tribomechanical properties of the periostracum of Mytilus sp(Amsterdam : Elsevier, 2014) Wählisch, Felix C.; Peter, Nicolas J.; Torrents Abad, Oscar; Oliveira, Mariana V.G.; Schneider, Andreas S.; Schmahl, Wolfgang; Griesshaber, Erika; Bennewitz, RolandWe investigated the friction and wear behavior as well as the mechanical properties of the periostracum of Mytilus sp. Tribological properties were determined with a reciprocal sliding microtribometer, while mechanical characterization was performed using a nanoindenter. Measurements were performed in dry and wet conditions. On the dry periostracum we found a low friction coefficient of 0.078 ± 0.007 on the young parts and a higher one of 0.63 ± 0.02 on the old parts of the shell. Under wet, saline, conditions we only observed one average coefficient of friction of 0.37 ± 0.01. Microscopic ex situ analysis indicated that dry periostracum wore rather rapidly by plowing and fatigue, while it exhibited a high wear resistance when immersed in salt water. The Young’s modulus and hardness of the periostracum were also investigated in both dry and wet conditions. Under dry conditions the Young’s modulus of the periostracum was 8 ± 3 GPa, while under wet conditions it was 0.21 ± 0.05 GPa. The hardness of dry periostracum samples was 353 ± 127 MPa, whereas the hardness of wet samples was 5 ± 2 MPa. It was found that, in the wet state, viscous behavior plays a significant role in the mechanical response of the periostracum. Our results strongly indicate that the periostracum can provide an important contribution to the overall wear resistance of Mytilus sp. shell.
- ItemHow to minimize dye-induced perturbations while studying biomembrane structure and dynamics: PEG linkers as a rational alternative(Amsterdam : Elsevier, 2018) Mobarak, Edouard; Javanainen, Matti; Kulig, Waldemar; Honigmann, Alf; Sezgin, Erdinc; Aho, Noora; Eggeling, Christian; Rog, Tomasz; Vattulainen, IlpoOrganic dye-tagged lipid analogs are essential for many fluorescence-based investigations of complex membrane structures, especially when using advanced microscopy approaches. However, lipid analogs may interfere with membrane structure and dynamics, and it is not obvious that the properties of lipid analogs would match those of non-labeled host lipids. In this work, we bridged atomistic simulations with super-resolution imaging experiments and biomimetic membranes to assess the performance of commonly used sphingomyelin-based lipid analogs. The objective was to compare, on equal footing, the relative strengths and weaknesses of acyl chain labeling, headgroup labeling, and labeling based on poly-ethyl-glycol (PEG) linkers in determining biomembrane properties. We observed that the most appropriate strategy to minimize dye-induced membrane perturbations and to allow consideration of Brownian-like diffusion in liquid-ordered membrane environments is to decouple the dye from a membrane by a PEG linker attached to a lipid headgroup. Yet, while the use of PEG linkers may sound a rational and even an obvious approach to explore membrane dynamics, the results also suggest that the dyes exploiting PEG linkers interfere with molecular interactions and their dynamics. Overall, the results highlight the great care needed when using fluorescent lipid analogs, in particular accurate controls.