Shaping Giant Membrane Vesicles in 3D-Printed Protein Hydrogel Cages

Giant unilamellar phospholipid vesicles are attractive starting points for constructing minimal living cells from the bottom-up. Their membranes are compatible with many physiologically functional modules and act as selective barriers, while retaining a high morphological flexibility. However, their spherical shape renders them rather inappropriate to study phenomena that are based on distinct cell shape and polarity, such as cell division. Here, a microscale device based on 3D printed protein hydrogel is introduced to induce pH-stimulated reversible shape changes in trapped vesicles without compromising their free-standing membranes. Deformations of spheres to at least twice their aspect ratio, but also toward unusual quadratic or triangular shapes can be accomplished. Mechanical force induced by the cages to phase-separated membrane vesicles can lead to spontaneous shape deformations, from the recurrent formation of dumbbells with curved necks between domains to full budding of membrane domains as separate vesicles. Moreover, shape-tunable vesicles are particularly desirable when reconstituting geometry-sensitive protein networks, such as reaction-diffusion systems. In particular, vesicle shape changes allow to switch between different modes of self-organized protein oscillations within, and thus, to influence reaction networks directly by external mechanical cues

Real-scale investigation of the kinematic response of a rockfall protection embankment

This paper addresses the response of rockfall protection embankments when exposed to a rock impact. For this purpose, real-scale impact experiments were conducted with impact energies ranging from 200 to 2200 kJ. The structure was composed of a 4m high cellular wall leaned against a levee. The wall was a double-layer sandwich made from gabion cages filled with either stones or a sand–schreddedtyre mixture. For the first time, sensors were placed in different locations within the structure to measure real-time accelerations and displacements. The test conditions, measurement methods and results are presented in detail. The structure’s response is discussed in a descriptive and phenomenological approach and compared with previous real-scale experiments on other types of embankments

Long-term analysis of carbon dioxide and methane column-averaged mole fractions retrieved from SCIAMACHY

Carbon dioxide (CO<sub>2</sub>) and methane (CH<sub>4</sub>) are the two most important anthropogenic greenhouse gases contributing to global climate change. SCIAMACHY onboard ENVISAT (launch 2002) was the first and is now with TANSO onboard GOSAT (launch 2009) one of only two satellite instruments currently in space whose measurements are sensitive to CO<sub>2</sub> and CH<sub>4</sub> concentration changes in the lowest atmospheric layers where the variability due to sources and sinks is largest. <br><br> We present long-term SCIAMACHY retrievals (2003–2009) of column-averaged dry air mole fractions of both gases (denoted XCO<sub>2</sub> and XCH<sub>4</sub>) derived from absorption bands in the near-infrared/shortwave-infrared (NIR/SWIR) spectral region focusing on large-scale features. The results are obtained using an upgraded version (v2) of the retrieval algorithm WFM-DOAS including several improvements, while simultaneously maintaining its high processing speed. The retrieved mole fractions are compared to global model simulations (CarbonTracker XCO<sub>2</sub> and TM5 XCH<sub>4</sub>) being optimised by assimilating highly accurate surface measurements from the NOAA/ESRL network and taking the SCIAMACHY averaging kernels into account. The comparisons address seasonal variations and long-term characteristics. <br><br> The steady increase of atmospheric carbon dioxide primarily caused by the burning of fossil fuels can be clearly observed with SCIAMACHY globally. The retrieved global annual mean XCO<sub>2</sub> increase agrees with CarbonTracker within the error bars (1.80±0.13 ppm yr<sup>−1</sup> compared to 1.81±0.09 ppm yr<sup>−1</sup>). The amplitude of the XCO<sub>2</sub> seasonal cycle as retrieved by SCIAMACHY, which is 4.3±0.2 ppm for the Northern Hemisphere and 1.4±0.2 ppm for the Southern Hemisphere, is on average about 1 ppm larger than for CarbonTracker. <br><br> An investigation of the boreal forest carbon uptake during the growing season via the analysis of longitudinal gradients shows good agreement between SCIAMACHY and CarbonTracker concerning the overall magnitude of the gradients and their annual variations. The analysis includes a discussion of the relative uptake strengths of the Russian and North American boreal forest regions. <br><br> The retrieved XCH<sub>4</sub> results show that after years of stability, atmospheric methane has started to rise again in recent years which is consistent with surface measurements. The largest increase is observed for the tropics and northern mid- and high-latitudes amounting to about 7.5±1.5 ppb yr<sup>−1</sup> since 2007. Due care has been exercised to minimise the influence of detector degradation on the quantitative estimate of this anomaly

Unstable Attractors: Existence and Robustness in Networks of Oscillators With Delayed Pulse Coupling

We consider unstable attractors; Milnor attractors $A$ such that, for some neighbourhood $U$ of $A$, almost all initial conditions leave $U$. Previous research strongly suggests that unstable attractors exist and even occur robustly (i.e. for open sets of parameter values) in a system modelling biological phenomena, namely in globally coupled oscillators with delayed pulse interactions. In the first part of this paper we give a rigorous definition of unstable attractors for general dynamical systems. We classify unstable attractors into two types, depending on whether or not there is a neighbourhood of the attractor that intersects the basin in a set of positive measure. We give examples of both types of unstable attractor; these examples have non-invertible dynamics that collapse certain open sets onto stable manifolds of saddle orbits. In the second part we give the first rigorous demonstration of existence and robust occurrence of unstable attractors in a network of oscillators with delayed pulse coupling. Although such systems are technically hybrid systems of delay differential equations with discontinuous `firing' events, we show that their dynamics reduces to a finite dimensional hybrid system system after a finite time and hence we can discuss Milnor attractors for this reduced finite dimensional system. We prove that for an open set of phase resetting functions there are saddle periodic orbits that are unstable attractors.Comment: 29 pages, 8 figures,submitted to Nonlinearit

Trusted CI Experiences in Cybersecurity and Service to Open Science

This article describes experiences and lessons learned from the Trusted CI project, funded by the US National Science Foundation to serve the community as the NSF Cybersecurity Center of Excellence. Trusted CI is an effort to address cybersecurity for the open science community through a single organization that provides leadership, training, consulting, and knowledge to that community. The article describes the experiences and lessons learned of Trusted CI regarding both cybersecurity for open science and managing the process of providing centralized services to a broad and diverse community.Comment: 8 pages, PEARC '19: Practice and Experience in Advanced Research Computing, July 28-August 1, 2019, Chicago, IL, US

Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.

Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins.Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven protonpump bacteriorhodopsin (bR) at a resolution of 2.4 A ° . The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway

A cascaded laser acceleration scheme for the generation of spectrally controlled proton beams

We present a novel, cascaded acceleration scheme for the generation of spectrally controlled ion beams using a laser-based accelerator in a 'double-stage' setup. An MeV proton beam produced during a relativistic laser–plasma interaction on a thin foil target is spectrally shaped by a secondary laser–plasma interaction on a separate foil, reliably creating well-separated quasi-monoenergetic features in the energy spectrum. The observed modulations are fully explained by a one-dimensional (1D) model supported by numerical simulations. These findings demonstrate that laser acceleration can, in principle, be applied in an additive manner.Deutsche Forschungsgemeinschaft (DFG contract no. TR18)Deutsche Forschungsgemeinschaft (contract no. 03ZIK052)European Union (Laserlab Europe

The Greenhouse Gas Climate Change Initiative (GHG-CCI): comparative validation of GHG-CCI SCIAMACHY/ENVISAT and TANSO-FTS/GOSAT CO₂ and CH₄ retrieval algorithm products with measurements from the TCCON

Column-averaged dry-air mole fractions of carbon dioxide and methane have been retrieved from spectra acquired by the TANSO-FTS (Thermal And Near-infrared Sensor for carbon Observations-Fourier Transform Spectrometer) and SCIAMACHY (Scanning Imaging Absorption Spectrometer for Atmospheric Cartography) instruments on board GOSAT (Greenhouse gases Observing SATellite) and ENVISAT (ENVIronmental SATellite), respectively, using a range of European retrieval algorithms. These retrievals have been compared with data from ground-based high-resolution Fourier transform spectrometers (FTSs) from the Total Carbon Column Observing Network (TCCON). The participating algorithms are the weighting function modified differential optical absorption spectroscopy (DOAS) algorithm (WFMD, University of Bremen), the Bremen optimal estimation DOAS algorithm (BESD, University of Bremen), the iterative maximum a posteriori DOAS (IMAP, Jet Propulsion Laboratory (JPL) and Netherlands Institute for Space Research algorithm (SRON)), the proxy and full-physics versions of SRON's RemoTeC algorithm (SRPR and SRFP, respectively) and the proxy and full-physics versions of the University of Leicester's adaptation of the OCO (Orbiting Carbon Observatory) algorithm (OCPR and OCFP, respectively). The goal of this algorithm inter-comparison was to identify strengths and weaknesses of the various so-called round- robin data sets generated with the various algorithms so as to determine which of the competing algorithms would proceed to the next round of the European Space Agency's (ESA) Greenhouse Gas Climate Change Initiative (GHG-CCI) project, which is the generation of the so-called Climate Research Data Package (CRDP), which is the first version of the Essential Climate Variable (ECV) "greenhouse gases" (GHGs). For XCO₂, all algorithms reach the precision requirements for inverse modelling (< 8 ppm), with only WFMD having a lower precision (4.7 ppm) than the other algorithm products (2.4–2.5 ppm). When looking at the seasonal relative accuracy (SRA, variability of the bias in space and time), none of the algorithms have reached the demanding < 0.5 ppm threshold. For XCH₄, the precision for both SCIAMACHY products (50.2 ppb for IMAP and 76.4 ppb for WFMD) fails to meet the < 34 ppb threshold for inverse modelling, but note that this work focusses on the period after the 2005 SCIAMACHY detector degradation. The GOSAT XCH₄ precision ranges between 18.1 and 14.0 ppb. Looking at the SRA, all GOSAT algorithm products reach the < 10 ppm threshold (values ranging between 5.4 and 6.2 ppb). For SCIAMACHY, IMAP and WFMD have a SRA of 17.2 and 10.5 ppb, respectively

Computational model combined with in vitro experiments to analyse mechanotransduction during mesenchymal stem cell adhesion.

The shape that stem cells reach at the end of adhesion process influences their differentiation. Rearrangement of cytoskeleton and modification of intracellular tension may activate mechanotransduction pathways controlling cell commitment. In the present study, the mechanical signals involved in cell adhesion were computed in in vitro stem cells of different shapes using a single cell model, the so-called Cytoskeleton Divided Medium (CDM) model. In the CDM model, the filamentous cytoskeleton and nucleoskeleton networks were represented as a mechanical system of multiple tensile and compressive interactions between the nodes of a divided medium. The results showed that intracellular tonus, focal adhesion forces as well as nuclear deformation increased with cell spreading. The cell model was also implemented to simulate the adhesion process of a cell that spreads on protein-coated substrate by emitting filopodia and creating new distant focal adhesion points. As a result, the cell model predicted cytoskeleton reorganisation and reinforcement during cell spreading. The present model quantitatively computed the evolution of certain elements of mechanotransduction and may be a powerful tool for understanding cell mechanobiology and designing biomaterials with specific surface properties to control cell adhesion and differentiation