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We present a setup combining a liquid flatjet sample delivery and a MHz laser system for time-resolved soft X-ray absorption measurements of liquid samples at the high brilliance undulator beamline UE52-SGM at Bessy II yielding unprecedented statistics in this spectral range. We demonstrate that the efficient detection of transient absorption changes in transmission mode enables the identification of photoexcited species in dilute samples. With iron(II)-trisbipyridine in aqueous solution as a benchmark system, we present absorption measurements at various edges in the soft X-ray regime. In combination with the wavelength tunability of the laser system, the set-up opens up opportunities to study the photochemistry of many systems at low concentrations, relevant to materials sciences, chemistry, and biology.
Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.
In Near Edge X-Ray Absorption Fine Structure (NEXAFS) spectroscopy X-Ray photons are used to excite tightly bound core electrons to low-lying unoccupied orbitals of the system. This technique offers insight into the electronic structure of the system as well as useful structural information. In this work, we apply NEXAFS to two kinds of imidazolium based ionic liquids ([CnC1im]+[NTf2]- and [C4C1im]+[I]-). A combination of measurements and quantum chemical calculations of C K and N K NEXAFS resonances is presented. The simulations, based on the transition potential density functional theory method (TP-DFT), reproduce all characteristic features observed by the experiment. Furthermore, a detailed assignment of resonance features to excitation centers (carbon or nitrogen atoms) leads to a consistent interpretation of the spectra.
Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein
(2020)
Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.
Modeling random crawling, membrane deformation and intracellular polarity of motile amoeboid cells
(2018)
Amoeboid movement is one of the most widespread forms of cell motility that plays a key role in numerous biological contexts. While many aspects of this process are well investigated, the large cell-to-cell variability in the motile characteristics of an otherwise uniform population remains an open question that was largely ignored by previous models. In this article, we present a mathematical model of amoeboid motility that combines noisy bistable kinetics with a dynamic phase field for the cell shape. To capture cell-to-cell variability, we introduce a single parameter for tuning the balance between polarity formation and intracellular noise. We compare numerical simulations of our model to experiments with the social amoeba Dictyostelium discoideum. Despite the simple structure of our model, we found close agreement with the experimental results for the center-of-mass motion as well as for the evolution of the cell shape and the overall intracellular patterns. We thus conjecture that the building blocks of our model capture essential features of amoeboid motility and may serve as a starting point for more detailed descriptions of cell motion in chemical gradients and confined environments.