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- ItemThe 2018 correlative microscopy techniques roadmap(Bristol : IOP Publishing, 2018) Ando, Toshio; Bhamidimarri, Satya Prathyusha; Brending, Niklas; Colin-York, H; Collinson, Lucy; De Jonge, Niels; de Pablo, P J; Debroye, Elke; Eggeling, Christian; Franck, Christian; Fritzsche, Marco; Gerritsen, Hans; Giepmans, Ben N G; Grunewald, Kay; Hofkens, Johan; Hoogenboom, Jacob P; Janssen, Kris P F; Kaufmann, Rainer; Klumpermann, Judith; Kurniawan, Nyoman; Kusch, Jana; Liv, Nalan; Parekh, Viha; Peckys, Diana B; Rehfeldt, Florian; Reutens, David C; Roeffaers, Maarten B J; Salditt, Tim; Schaap, Iwan A T; Schwarz, Ulrich S; Verkade, Paul; Vogel, Michael W; Wagner, Richard; Winterhalter, Mathias; Yuan, Haifeng; Zifarelli, GiovanniDevelopments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell–cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure–function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.
- ItemDoppler-free spectroscopy with a terahertz quantum-cascade laser(Washington, DC : Optical Society of America, 2018) Wienold, M.; Alam, T.; Schrottke, L.; Grahn, H.T.; Hübers, H.-W.We report on the Doppler-free saturation spectroscopy of a molecular transition at 3.3 THz based on a quantum-cascade laser and an absorption cell in a collinear pump-probe configuration. A Lamb dip with a sub-Doppler linewidth of 170 kHz is observed for a rotational transition of HDO. We found that a certain level of external optical feedback is tolerable as long as the free spectral range of the external cavity is large compared to the width of the absorption line.
- ItemUsing machine-learning to optimize phase contrast in a low-cost cellphone microscope(San Francisco, CA : Public Library of Science, 2018) Diederich, Benedict; Wartmann, Rolf; Schadwinkel, Harald; Heintzmann, RainerCellphones equipped with high-quality cameras and powerful CPUs as well as GPUs are widespread. This opens new prospects to use such existing computational and imaging resources to perform medical diagnosis in developing countries at a very low cost. Many relevant samples, like biological cells or waterborn parasites, are almost fully transparent. As they do not exhibit absorption, but alter the light’s phase only, they are almost invisible in brightfield microscopy. Expensive equipment and procedures for microscopic contrasting or sample staining often are not available. Dedicated illumination approaches, tailored to the sample under investigation help to boost the contrast. This is achieved by a programmable illumination source, which also allows to measure the phase gradient using the differential phase contrast (DPC) [1, 2] or even the quantitative phase using the derived qDPC approach [3]. By applying machine-learning techniques, such as a convolutional neural network (CNN), it is possible to learn a relationship between samples to be examined and its optimal light source shapes, in order to increase e.g. phase contrast, from a given dataset to enable real-time applications. For the experimental setup, we developed a 3D-printed smartphone microscope for less than 100 $ using off-the-shelf components only such as a low-cost video projector. The fully automated system assures true Koehler illumination with an LCD as the condenser aperture and a reversed smartphone lens as the microscope objective. We show that the effect of a varied light source shape, using the pre-trained CNN, does not only improve the phase contrast, but also the impression of an improvement in optical resolution without adding any special optics, as demonstrated by measurements.
- ItemNatural variation in physiological responses of tunisian hedysarum carnosum under iron deficiency(Lausanne : Frontiers Media, 2018) Abdallah, Heithem Ben; Mai, Hans Jörg; Slatni, Tarek; Fink-Straube, Claudia; Abdelly, Chedly; Bauer, PetraIron (Fe) is an essential element for plant growth and development. The cultivation of leguminous plants has generated strong interest because of their growth even on poor soils. Calcareous and saline soils with poor mineral availability are wide-spread in Tunisia. In an attempt to select better forage crops adapted to Tunisian soils, we characterized Fe deficiency responses of three different isolates of Hedysarum carnosum, an endemic Tunisian extremophile species growing in native stands in salt and calcareous soil conditions. H. carnosum is a non-model crop. The three isolates, named according to their habitats Karkar, Thelja, and Douiret, differed in the expression of Fe deficiency symptoms like morphology, leaf chlorosis with compromised leaf chlorophyll content and photosynthetic capacity and leaf metal contents. Across these parameters Thelja was found to be tolerant, while Karkar and Douiret were susceptible to Fe deficiency stress. The three physiological and molecular indicators of the iron deficiency response in roots, Fe reductase activity, growth medium acidification and induction of the IRON-REGULATED TRANSPORTER1 homolog, indicated that all lines responded to -Fe, however, varied in the strength of the different responses. We conclude that the individual lines have distinct adaptation capacities to react to iron deficiency, presumably involving mechanisms of whole-plant iron homeostasis and internal metal distribution. The Fe deficiency tolerance of Thelja might be linked with adaptation to its natural habitat on calcareous soil.
- ItemImplementation of safe-by-design for nanomaterial development and safe innovation: Why we need a comprehensive approach(Basel : MDPI, 2018) Kraegeloh, Annette; Suarez-Merino, Blanca; Sluijter, Teun; Micheletti, ChristianManufactured nanomaterials (MNMs) are regarded as key components of innovations in various fields with high potential impact (e.g., energy generation and storage, electronics, photonics, diagnostics, theranostics, or drug delivery agents). Widespread use of MNMs raises concerns about their safety for humans and the environment, possibly limiting the impact of the nanotechnology-based innovation. The development of safe MNMs and nanoproducts has to result in a safe as well as functional material or product. Its safe use, and disposal at the end of its life cycle must be taken into account too. However, not all MNMs are similarly useful for all applications, some might bear a higher hazard potential than others, and use scenarios could lead to different exposure probabilities. To improve both safety and efficacy of nanotechnology, we think that a new proactive approach is necessary, based on pre-regulatory safety assessment and dialogue between stakeholders. On the basis of the work carried out in different European Union (EU) initiatives, developing and integrating MNMs Safe-by-Design and Trusted Environments (NANoREG, ProSafe, and NanoReg2), we present our point of view here. This concept, when fully developed, will allow for cost effective industrial innovation, and an exchange of key information between regulators and innovators. Regulators are thus informed about incoming innovations in good time, supporting a proactive regulatory action. The final goal is to contribute to the nanotechnology governance, having faster, cheaper, effective, and safer nano-products on the market.
- ItemOrdered states in the Kitaev-Heisenberg model: From 1D chains to 2D honeycomb(London : Nature Publishing Group, 2018) Agrapidis, Cliò Efthimia; van den Brink, Jeroen; Nishimoto, SatoshiWe study the ground state of the 1D Kitaev-Heisenberg (KH) model using the density-matrix renormalization group and Lanczos exact diagonalization methods. We obtain a rich ground-state phase diagram as a function of the ratio between Heisenberg (J = cosϕ) and Kitaev (K = sinϕ) interactions. Depending on the ratio, the system exhibits four long-range ordered states: ferromagnetic-z, ferromagnetic-xy, staggered-xy, Néel-z, and two liquid states: Tomonaga-Luttinger liquid and spiral-xy. The two Kitaev points ϕ=π2 and φ=3π2 are singular. The ϕ-dependent phase diagram is similar to that for the 2D honeycomb-lattice KH model. Remarkably, all the ordered states of the honeycomb-lattice KH model can be interpreted in terms of the coupled KH chains. We also discuss the magnetic structure of the K-intercalated RuCl3, a potential Kitaev material, in the framework of the 1D KH model. Furthermore, we demonstrate that the low-lying excitations of the 1D KH Hamiltonian can be explained within the combination of the known six-vertex model and spin-wave theory.
- ItemAntarctic sub-shelf melt rates via PICO(München : European Geopyhsical Union, 2018) Reese, Ronja; Albrecht, Torsten; Mengel, Matthias; Asay-Davis, Xylar; Winkelmann, RicardaOcean-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 m a−1 for cold sub-shelf cavities, for example, underneath Ross or Ronne ice shelves, to 16 m a−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.
- ItemSize control in mammalian cells involves modulation of both growth rate and cell cycle duration(London : Nature Publishing Group, 2018) Cadar, Clotilde; Monnier, Sylvain; Grilli, Jacopo; Sáez, Pablo J.; Srivastava, Nishit; Attia, Rafaele; Terriac, Emmanuel; Baum, Buzz; Cosentino-Lagomarsino, Marco; Piel, MatthieuDespite decades of research, how mammalian cell size is controlled remains unclear because of the difficulty of directly measuring growth at the single-cell level. Here we report direct measurements of single-cell volumes over entire cell cycles on various mammalian cell lines and primary human cells. We find that, in a majority of cell types, the volume added across the cell cycle shows little or no correlation to cell birth size, a homeostatic behavior called “adder”. This behavior involves modulation of G1 or S-G2 duration and modulation of growth rate. The precise combination of these mechanisms depends on the cell type and the growth condition. We have developed a mathematical framework to compare size homeostasis in datasets ranging from bacteria to mammalian cells. This reveals that a near-adder behavior is the most common type of size control and highlights the importance of growth rate modulation to size control in mammalian cells.
- ItemDesign and results of the ice sheet model initialisation experiments initMIP-Greenland: an ISMIP6 intercomparison(München : European Geopyhsical Union, 2018) Goelzer, Heiko; Nowicki, Sophie; Edwards, Tamsin; Beckley, Matthew; Abe-Ouchi, Ayako; Aschwanden, Andy; Calov, Reinhard; Gagliardini, Olivier; Gillet-Chaulet, Fabien; Golledge, Nicholas R.; Gregory, Jonathan; Greve, Ralf; Humbert, Angelika; Huybrechts, Philippe; Kennedy, Joseph H.; Larour, Eric; Lipscomb, William H.; Le clec'h, Sébastien; Lee, Victoria; Morlighem, Mathieu; Pattyn, Frank; Payne, Antony J.; Rodehacke, Christian; Martin Rückamp, Martin; Saito, Fuyuki; Schlegel, Nicole; Seroussi, Helene; Shepherd, Andrew; Sun, Sainan; van de Wal, Roderik; Ziemen, Florian A.Earlier large-scale Greenland ice sheet sea-level projections (e.g. those run during the ice2sea and SeaRISE initiatives) have shown that ice sheet initial conditions have a large effect on the projections and give rise to important uncertainties. The goal of this initMIP-Greenland intercomparison exercise is to compare, evaluate, and improve the initialisation techniques used in the ice sheet modelling community and to estimate the associated uncertainties in modelled mass changes. initMIP-Greenland is the first in a series of ice sheet model intercomparison activities within ISMIP6 (the Ice Sheet Model Intercomparison Project for CMIP6), which is the primary activity within the Coupled Model Intercomparison Project Phase 6 (CMIP6) focusing on the ice sheets. Two experiments for the large-scale Greenland ice sheet have been designed to allow intercomparison between participating models of (1) the initial present-day state of the ice sheet and (2) the response in two idealised forward experiments. The forward experiments serve to evaluate the initialisation in terms of model drift (forward run without additional forcing) and in response to a large perturbation (prescribed surface mass balance anomaly); they should not be interpreted as sea-level projections. We present and discuss results that highlight the diversity of data sets, boundary conditions, and initialisation techniques used in the community to generate initial states of the Greenland ice sheet. We find good agreement across the ensemble for the dynamic response to surface mass balance changes in areas where the simulated ice sheets overlap but differences arising from the initial size of the ice sheet. The model drift in the control experiment is reduced for models that participated in earlier intercomparison exercises.
- ItemComment on 'Oxygen vacancy-induced magnetic moment in edge-sharing CuO2 chains of Li2CuO2'(Bristol : IOP Publishing, 2018) Kuzian, R.O.; Klingeler, R.; Lorenz, W.E.A.; Wizent, N.; Nishimoto, S.; Nitzsche, U.; Rosner, H.; Milosavljevic, D.; Hozoi, L.; Yadav, R.; Richter, J.; Hauser, A.; Geck, J.; Hayn, R.; Yushankhai, V.; Siurakshina, L.; Monney, C.; Schmitt, T.; Schmitt, T.; Roth, G.; Ito, T.; Yamaguchi, H.; Matsuda, M.; Johnston, S.; Málek, J.; Drechsler, S.-L.In a recent work devoted to the magnetism of Li2CuO2, Shu et al (2017 New J. Phys. 19, 023026) have proposed a 'simplified' unfrustrated microscopic model that differs considerably from the models refined through decades of prior work. We show that the proposed model is at odds with known experimental data, including the reported magnetic susceptibility χ(T) data up to 550 K. Using an 8th order high-temperature expansion for χ(T), we show that the experimental data for Li2CuO2 are consistent with the prior model derived from inelastic neutron scattering studies. We also establish the T-range of validity for a Curie–Weiss law for the real frustrated magnetic system. We argue that the knowledge of the long-range ordered magnetic structure for T < T N and of χ(T) in a restricted T-range provides insufficient information to extract all of the relevant couplings in frustrated magnets; the saturation field and INS data must also be used to determine several exchange couplings, including the weak but decisive frustrating antiferromagnetic interchain couplings.