Recent Submissions

  • Journal Article

    Game of Zones: how actin-binding proteins organize muscle contraction 

    Butkevich, Eugenia; Klopfenstein, Dieter R.; Schmidt, Christoph F.
    Worm 2016; 5(2): Art. e1161880
    Locomotion of C. elegans requires coordinated, efficient transmission of forces generated on the molecular scale by myosin and actin filaments in myocytes to dense bodies and the hypodermis and cuticle enveloping body wall muscles. The complex organization of the acto-myosin scaffold with its accessory proteins provides a fine-tuned machinery regulated by effectors that guarantees that sarcomere units undergo controlled, reversible cycles of contraction and relaxation. Actin filaments in sarcomeres dynamically undergo polymerization and depolymerization. In a recent study, the actin-binding protein DBN-1, the C. elegans ortholog of human drebrin and drebrin-like proteins, was discovered to stabilize actin in muscle cells. DBN-1 reversibly changes location between actin filaments and myosin-rich regions during muscle contraction. Mutations in DBN-1 result in mislocalization of other actin-binding proteins. Here we discuss implications of this finding for the regulation of sarcomere actin stability and the organization of other actin-binding proteins.
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  • Journal Article

    Mapping Cellular Microenvironments: Proximity Labeling and Complexome Profiling (Seventh Symposium of the Göttingen Proteomics Forum) 

    Valerius, Oliver; Asif, Abdul R.; Beißbarth, Tim; Bohrer, Rainer; Dihazi, Hassan; Feussner, Kirstin; Jahn, Olaf; Majcherczyk, Andrzej; Schmidt, Bernhard; Schmitt, Kerstin; et al.
    Urlaub, HenningLenz, Christof
    Cells 2019; 8(10): Art. 1192
    Mass spectrometry-based proteomics methods are finding increasing use in structural biology research. Beyond simple interaction networks, information about stable protein-protein complexes or spatially proximal proteins helps to elucidate the biological functions of proteins in a wider cellular context. To shed light on new developments in this field, the Göttingen Proteomics Forum organized a one-day symposium focused on complexome profiling and proximity labeling, two emerging technologies that are gaining significant attention in biomolecular research. The symposium was held in Göttingen, Germany on 23 May, 2019, as part of a series of regular symposia organized by the Göttingen Proteomics Forum.
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  • Journal Article

    The Preparation and Preliminary Characterisation of Three Synthetic Andesite Reference Glass Materials (ARM‐1, ARM‐2, ARM‐3) for In Situ Microanalysis 

    Wu, Shitou; Wörner, Gerhard; Jochum, Klaus Peter; Stoll, Brigitte; Simon, Klaus; Kronz, Andreas
    Geostandards and Geoanalytical Research 2019; 43(4) p.567-584
    Three synthetic reference glasses were prepared by directly fusing and stirring 3.8 kg of high-purity oxide powders to provide reference materials for microanalytical work. These glasses have andesitic major compositions and are doped with fifty-four trace elements in nearly identical abundance (500, 50, 5 µg g-1) using oxide powders or element solutions, and are named ARM-1, 2 and 3, respectively. We further document that sector-field (SF) ICP-MS (Element 2 or Element XR) is capable of sweeping seventy-seven isotopes (from 7Li to 238U, a total of sixty-eight elements) in 1 s and, thus, is able to quantify up to sixty-eight elements by laser sampling. Micro- and bulk analyses indicate that the glasses are homogeneous with respect to major and trace elements. This paper provides preliminary data for the ARM glasses using a variety of analytical techniques (EPMA, XRF, ICP-OES, ICP-MS, LA-Q-ICP-MS and LA-SF-ICP-MS) performed in ten laboratories. Discrepancies in the data of V, Cr, Ni and Tl exist, mainly caused by analytical limitations. Preliminary reference and information values for fifty-six elements were calculated with uncertainties [2 relative standard error (RSE)] estimated in the range of 1–20%.
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  • Journal Article

    Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea 

    Braun, Katrin; Leubner, Fanny; Stach, Thomas
    Cladistics p.1-42
    With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA‐sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up‐weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free‐living and that ascidian sessility is a derived trait within Tunicata. “Thaliacea” is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic “Ascidiacea”. Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter‐relationships of this diverse marine taxon in a consistent cladistic framework.
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  • Journal Article

    Falloff curves and mechanism of thermal decomposition of CF3I in shock waves 

    Cobos, C. J.; Sölter, L.; Tellbach, E.; Troe, J.
    Physical Chemistry Chemical Physics 2019; 21(43) p.23893-23899
    The falloff curves of the unimolecular dissociation CF3I (+Ar) → CF3 + I (+Ar) are modelled by combining quantum-chemical characterizations of the potential energy surface for the reaction, standard unimolecular rate theory, and experimental information on the average energy transferred per collision between excited CF3I and Ar. The (essentially) parameter-free theoretical modelling gives results in satisfactory agreement with data deduced from earlier shock wave experiments employing a variety of reactant concentrations (between a few ppm and a few percent in the bath gas Ar). New experiments recording absorption-time signals of CF3I, I2, CF2 and (possibly) IF at 450-500 and 200-300 nm are reported. By analysing the decomposition mechanism, besides the unimolecular dissociation of CF3I, these provide insight into the influence of secondary reactions on the experimental observations.
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  • Journal Article

    Fattening Pig Farmers’ Intention to Participate in Animal Welfare Programs 

    Schukat; Kuhlmann; Heise
    Animals 2019; 9(12): Art. 1042
    Farmers are considered a highly important stakeholder group for the successful implementation of higher farm animal welfare (FAW) standards, but so far little is known about their attitudes and the determinants of their participation in programs that request higher FAW standards. To close this research gap, fattening pig farmers in Germany were questioned via a large-scale online survey in 2018 (n = 239). Based on the Unified Theory of Acceptance and Use of Technology, a partial least squares path modeling (PLS) was run. Results show that the expected performance as well as the expected costs associated with the Initiative Animal Welfare (IAW) substantially influence fattening pig farmers' behavioral intention to participate in the IAW. Furthermore, the decision is influenced by social determinants and facilitating conditions such as deadweight effects. Farmers' hedonic motivation, fair remuneration and previous experiences with the establishment of higher FAW standards can influence their intention to take part in the IAW. In addition, farmers' trust in the program is a major determinant. There are also moderating variables such as age and work experience that influence farmers' intention to take part in the IAW. Our results have important managerial implications for the IAW and can help to design further tailor-made animal welfare programs (AWPs) that fulfill the requirements of both fattening pig farmers and the broader public not only in Germany but the European Union.
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  • Journal Article

    The effectiveness of livestock protection measures against wolves (Canis lupus) and implications for their co-existence with humans 

    Bruns, Antonia; Waltert, Matthias; Khorozyan, Igor
    Global Ecology and Conservation 2020; 21: Art. e00868
    Wolves (Canis lupus) can kill domestic livestock resulting in intense conflicts with humans. Damage to livestock should be reduced to facilitate human-wolf coexistence and ensure positive outcomes of conservation efforts. Current knowledge on the effectiveness of livestock protection measures from wolves is limited and scattered in the literature. In this study, we compiled a dataset of 30 cases describing the application of 11 measures of protecting cattle and smaller livestock against wolves, estimated their effectiveness as a relative risk of damage, and identified the best measures for damage reduction. We found that: (1) lethal control and translocation were less effective than other measures, (2) deterrents, especially fladry which is a fence with ropes marked by hanging colored flags that sway in the wind and provide a visual warning signal, were more effective than guarding dogs; (3) deterrents, fencing, calving control and herding were very effective, but the last two measures included only one case each; and (4) protection of cattle was more effective than that of small stock (sheep and goats, or sheep only) and mixed cattle and small stock. In all of these cases, the relative risk of damage was reduced by 50–100%. Considering Germany as an example of a country with a recovering wolf population and escalating human-wolf conflicts, we suggest electric fences and electrified fladry as the most promising measures, which under suitable conditions can be accompanied by well-trained livestock guarding dogs, and the temporary use of deterrents during critical periods such as calving and lambing seasons. Further research in this field is of paramount importance to efficiently mitigate human-wolf conflicts.
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  • Journal Article

    Minimum magnesium concentrations for photosynthetic efficiency in wheat and sunflower seedlings 

    Tränkner, Merle; Jamali Jaghdani, Setareh
    Plant Physiology and Biochemistry 2019; 144 p.234-243
    Photosynthetic processes in the chloroplast depend on the abundance of magnesium (Mg) in relatively high amounts; hence chloroplasts might react more sensitive to Mg-deficiency than other physiological processes within other organelles. Most authors suggest a critical Mg concentration to be 1.5 mg g-1 DM for biomass and yield formation. However, it is not yet elucidated whether this value also applies to photosynthetic processes. The present study focused on the response of photosynthetic processes to different Mg tissue concentrations. Wheat (Triticum aestivum) and sunflower (Helianthus annuus) plants were grown hydroponically for 10 days with 8 different levels of Mg supply (1.0, 0.5, 0.25, 0.1, 0.075, 0.05, 0.025, 0.01 mM Mg). Specific leaf mass, SPAD values, assimilation rate, Fv/Fm, electron transport rate and photochemical and non-photochemical quenching parameters were determined on youngest mature leaves. Tissue Mg concentrations decreased with lowering Mg supply to lowest concentrations of 0.7 mg g-1 DM in wheat leaves, but photosynthetic capacity was not affected. In sunflower leaves, lowest Mg concentrations of 0.56 mg g-1 DM were achieved and a diminished photosynthetic capacity was observed. The study shows that a Mg tissue concentration of 1.5 mg g-1 DM did not induce a negative effect on the photosynthetic capacity of wheat and sunflower leaves under our experimental conditions and hence, the critical Mg concentration for photosynthetic processes might be lower than for biomass and yield formation.
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  • Journal Article

    The effect of bigger human bodies on the future global calorie requirements 

    Depenbusch, Lutz; Klasen, Stephan
    PLOS ONE 2019; 14(12): Art. e0223188
    Existing studies show how population growth and rising incomes will cause a massive increase in the future global demand for food. We add to the literature by estimating the potential effect of increases in human weight, caused by rising BMI and height, on future calorie requirements. Instead of using a market based approach, the estimations are solely based on human energy requirements for maintenance of weight. We develop four different scenarios to show the effect of increases in human height and BMI. In a world where the weight per age-sex group would stay stable, we project calorie requirements to increases by 61.05 percent between 2010 and 2100. Increases in BMI and height could add another 18.73 percentage points to this. This additional increase amounts to more than the combined calorie requirements of India and Nigeria in 2010. These increases would particularly affect Sub-Saharan African countries, which will already face massively rising calorie requirements due to the high population growth. The stark regional differences call for policies that increase food access in currently economically weak regions. Such policies should shift consumption away from energy dense foods that promote overweight and obesity, to avoid the direct burden associated with these conditions and reduce the increases in required calories. Supplying insufficient calories would not solve the problem but cause malnutrition in populations with weak access to food. As malnutrition is not reducing but promoting rises in BMI levels, this might even aggravate the situation
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  • Journal Article

    Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes 

    Sousa, Thiago de Jesus; Parise, Doglas; Profeta, Rodrigo; Parise, Mariana Teixeira Dornelles; Gomide, Anne Cybelle Pinto; Kato, Rodrigo Bentos; Pereira, Felipe Luiz; Figueiredo, Henrique Cesar Pereira; Ramos, Rommel; Brenig, Bertram; et al.
    Costa da Silva, Artur Luiz daGhosh, PreetamBarh, DebmalyaGóes-Neto, AristótelesAzevedo, Vasco
    Scientific Reports 2019; 9(1): Art. 16387
    The number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously. Also, the greatest challenge to the assembly progress is the presence of repetitive DNA regions. This article highlights the use of optical mapping, to detect and correct assembly errors in Corynebacterium pseudotuberculosis. We also demonstrate that choosing a reference genome should be done with caution to avoid assembly errors and loss of genetic information.
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  • Journal Article

    Regulation of priming effect by soil organic matter stability over a broad geographic scale 

    Chen, Leiyi; Liu, Li; Qin, Shuqi; Yang, Guibiao; Fang, Kai; Zhu, Biao; Kuzyakov, Yakov; Chen, Pengdong; Xu, Yunping; Yang, Yuanhe
    Nature Communications 2019; 10(1): Art. 5112
    The modification of soil organic matter (SOM) decomposition by plant carbon (C) input (priming effect) represents a critical biogeochemical process that controls soil C dynamics. However, the patterns and drivers of the priming effect remain hidden, especially over broad geographic scales under various climate and soil conditions. By combining systematic field and laboratory analyses based on multiple analytical and statistical approaches, we explore the determinants of priming intensity along a 2200 km grassland transect on the Tibetan Plateau. Our results show that SOM stability characterized by chemical recalcitrance and physico-chemical protection explains more variance in the priming effect than plant, soil and microbial properties. High priming intensity (up to 137% of basal respiration) is associated with complex SOM chemical structures and low mineral-organic associations. The dependence of priming effect on SOM stabilization mechanisms should be considered in Earth System Models to accurately predict soil C dynamics under changing environments.
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  • Journal Article

    OH defect contents in quartz in a granitic system at 1–5 kbar 

    Potrafke, Alexander; Stalder, Roland; Schmidt, Burkhard C.; Ludwig, Thomas
    Contributions to Mineralogy and Petrology 2019; 174(12)
    Quartz is able to incorporate trace elements (e.g., H, Li, Al, B) depending on the formation conditions (P, T, and chemical system). Consequently, quartz can be used as a tracer for petrogenetic information of silicic plutonic bodies. In this experimental study, we provide the first data set on the OH defect incorporation in quartz from granites over a pressure/temperature range realistic for the emplacement of granitic melts in the upper crust. Piston cylinder and internally heated pressure vessel synthesis experiments were performed in a water-saturated granitic system at 1-5 kbar and 700-950 °C. Crystals from successful runs were analysed by secondary ion mass spectrometry (SIMS) and Fourier transform infrared (FTIR) spectroscopy, and their homogeneity was verified by FTIR imaging. IR absorption bands can be assigned to specific OH defects and analysed qualitatively and quantitatively and reveal that (1) the AlOH band triplet at 3310, 3378 and 3430 cm-1 is the dominating absorption feature in all spectra, (2) no simple trend of total OH defect incorporation with pressure can be observed, (3) the LiOH defect band at 3470-3480 cm-1 increases strongly in a narrow pressure interval from 4 kbar (220 µg/g H2O) to 4.5 kbar (500 µg/g H2O), and declines equally strong towards 5 kbar (180 µg/g H2O). Proton incorporation is charge balanced according to the equation H+ + A+ + P5+ = M3+ + B3+, with A+ = alkali ions and M3+ = trivalent metal ions.
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  • Journal Article

    The contribution of bacterial genome engineering to sustainable development 

    Reuß, Daniel R.; Commichau, Fabian M.; Stülke, Jörg
    Microbial Biotechnology 2017; 10(5) p.1259-1263
    The United Nations' Sustainable Development Goals define important challenges for the prosperous development of mankind. To reach several of these goals, among them the production of value-added compounds, improved economic and ecologic balance of production processes, prevention of climate change and protection of ecosystems, the use of engineered bacteria can make valuable contributions. We discuss the strategies for genome engineering and how they can be applied to meet the United Nations' goals for sustainable development.
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  • Journal Article

    Using invariom modelling to distinguish correct and incorrect central atoms in `duplicate structures' with neighbouring 3 d elements 

    Wandtke, Claudia M.; Weil, Matthias; Simpson, Jim; Dittrich, Birger
    Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 2017; 73(5) p.794-804
    Modelling coordination compounds has been shown to be feasible using the invariom method; for the best fit to a given set of diffraction data, additional steps other than using lookup tables of scattering factors need to be carried out. Here such procedures are applied to a number of `duplicate structures', where structures of two or more supposedly different coordination complexes with identical ligand environments, but with different 3d metal ions, were published. However, only one metal atom can be plausibly correct in these structures, and other spectroscopic data are unavailable. Using aspherical scattering factors, a structure can be identified as correct from the deposited Bragg intensities alone and modelling only the ligand environment often suffices to make this distinction. This is not possible in classical refinements using the independent atom model. Quantum-chemical computations of the better model obtained after aspherical-atom refinement further confirm the assignment of the element in the respective figures of merit.
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  • Journal Article

    Three-Dimensional Spatiotemporal Pulse-Train Solitons 

    Lahav, Oren; Kfir, Ofer; Sidorenko, Pavel; Mutzafi, Maor; Fleischer, Avner; Cohen, Oren
    Physical Review X 2017; 7(4)
    Experimental realization of three-dimensional spatiotemporal solitons, which were proposed several decades ago, is still considered a “grand challenge” in nonlinear science. Here, we present experimental observation of 3D optical spatiotemporal pulse-train solitons. A spatially bright temporally dark pulse-train beam is trapped in a bulk medium that supports two types of nonlinearities: slowly responding saturable self-focusing that collectively self-trap the beam in the transverse directions and fast self-phase modulation that self-localizes each dark notch temporally (longitudinally). This work opens the possibility for experimental investigations of various soliton phenomena, including soliton interaction in 3D, formation of multimode spatiotemporal solitons, and envisioning new entities like partially coherent spatiotemporal solitons.
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    Efficient phenotypic sex classification of zebrafish using machine learning methods 

    Hosseini, Shahrbanou; Simianer, Henner; Tetens, Jens; Brenig, Bertram; Herzog, Sebastian; Sharifi, Ahmad Reza
    Ecology and Evolution p.1-12
    Sex determination in zebrafish by manual approaches according to current guidelines relies on human observation. These guidelines for sex recognition have proven to be subjective and highly labor‐intensive. To address this problem, we present a methodology to automatically classify the phenotypic sex using two machine learning methods: Deep Convolutional Neural Networks (DCNNs) based on the whole fish appearance and Support Vector Machine (SVM) based on caudal fin coloration. Machine learning techniques in sex classification provide potential efficiency with the advantage of automatization and robustness in the prediction process. Furthermore, since developmental plasticity can be influenced by environmental conditions, we have investigated the impact of elevated water temperature during embryogenesis on sex and sex‐related differences in color intensity of adult zebrafish. The estimated color intensity based on SVM was then applied to detect the association between coloration and body weight and length. Phenotypic sex classifications using machine learning methods resulted in a high degree of association with the real sex in nontreated animals. In temperature‐induced animals, DCNNs reached a performance of 100%, whereas 20% of males were misclassified using SVM due to a lower color intensity. Furthermore, a positive association between color intensity and body weight and length was observed in males. Our study demonstrates that high ambient temperature leads to a lower color intensity in male animals and a positive association of male caudal fin coloration with body weight and length, which appears to play a significant role in sexual attraction. The software developed for sex classification in this study is readily applicable to other species with sex‐linked visible phenotypic differences.
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  • Journal Article

    Hydridoorganostannylene Coordination: Group 4 Metallocene Dichloride Reduction in Reaction with Organodihydridostannate Anions 

    Maudrich, Jakob‐Jonathan; Widemann, Max; Diab, Fatima; Kern, Ralf H.; Sirsch, Peter; Sindlinger, Christian P.; Schubert, Hartmut; Wesemann, Lars
    Chemistry – A European Journal(25) p.1-8
    Organodihydridoelement anions of germanium and tin were reacted with metallocene dichlorides of Group 4 metals Ti, Zr and Hf. The germate anion [Ar*GeH2 ]- reacts with hafnocene dichloride under formation of the substitution product [Cp2 Hf(GeH2 Ar*)2 ]. Reaction of the organodihydridostannate with metallocene dichlorides affords the reduction products [Cp2 M(SnHAr*)2 ] (M=Ti, Zr, Hf). Abstraction of a hydride substituent from the titanium bis(hydridoorganostannylene) complex results in formation of cation [Cp2 M(SnAr*)(SnHAr*)]+ exhibiting a short Ti-Sn interaction. (Ar*=2,6-Trip2 C6 H3 , Trip=2,4,6-triisopropylphenyl).
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  • Journal Article

    Measurement of Angstrom to Nanometer Molecular Distances with 19 F Nuclear Spins by EPR/ENDOR Spectroscopy 

    Meyer, Andreas; Dechert, Sebastian; Dey, Surjendu; Höbartner, Claudia; Bennati, Marina
    Angewandte Chemie International Edition(58) p.2-9
    Spectroscopic and biophysical methods for structural determination at atomic resolution are fundamental in studies of biological function. Here we introduce an approach to measure molecular distances in bio-macromolecules using 19 F nuclear spins and nitroxide radicals in combination with high-frequency (94 GHz/3.4 T) electron-nuclear double resonance (ENDOR). The small size and large gyromagnetic ratio of the 19 F label enables to access distances up to about 1.5 nm with an accuracy of 0.1-1 Å. The experiment is not limited by the size of the bio-macromolecule. Performance is illustrated on synthesized fluorinated model compounds as well as spin-labelled RNA duplexes. The results demonstrate that our simple but strategic spin-labelling procedure combined with state-of-the-art spectroscopy accesses a distance range crucial to elucidate active sites of nucleic acids or proteins in the solution state.
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  • Journal Article

    Antifreezing Hydrogel with High Zinc Reversibility for Flexible and Durable Aqueous Batteries by Cooperative Hydrated Cations 

    Zhu, Minshen; Wang, Xiaojie; Tang, Hongmei; Wang, Jiawei; Hao, Qi; Liu, Lixiang; Li, Yang; Zhang, Kai; Schmidt, Oliver G.
    Advanced Functional Materials: Art. 1907218
    Hydrogels are widely used in flexible aqueous batteries due to their liquid-like ion transportation abilities and solid-like mechanical properties. Their potential applications in flexible and wearable electronics introduce a fundamental challenge: how to lower the freezing point of hydrogels to preserve these merits without sacrificing hydrogels’ basic advantages in low cost and high safety. Moreover, zinc as an ideal anode in aqueous batteries suffers from low reversibility because of the formation of insulative byproducts, which is mainly caused by hydrogen evolution via extensive hydration of zinc ions. This, in principle, requires the suppression of hydration, which induces an undesirable increase in the freezing point of hydrogels. Here, it is demonstrated that cooperatively hydrated cations, zinc and lithium ions in hydrogels, are very effective in addressing the above challenges. This simple but unique hydrogel not only enables a 98% capacity retention upon cooling down to −20 °C from room temperature but also allows a near 100% capacity retention with >99.5% Coulombic efficiency over 500 cycles at −20 °C. In addition, the strengthened mechanical properties of the hydrogel under subzero temperatures result in excellent durability under various harsh deformations after the freezing process.
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