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Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood.
Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes.
Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.
Dimensional psychiatry
(2014)
A dimensional approach in psychiatry aims to identify core mechanisms of mental disorders across nosological boundaries.
We compared anticipation of reward between major psychiatric disorders, and investigated whether reward anticipation is impaired in several mental disorders and whether there is a common psychopathological correlate (negative mood) of such an impairment.
We used functional magnetic resonance imaging (fMRI) and a monetary incentive delay (MID) task to study the functional correlates of reward anticipation across major psychiatric disorders in 184 subjects, with the diagnoses of alcohol dependence (n = 26), schizophrenia (n = 44), major depressive disorder (MDD, n = 24), bipolar disorder (acute manic episode, n = 13), attention deficit/hyperactivity disorder (ADHD, n = 23), and healthy controls (n = 54). Subjects' individual Beck Depression Inventory-and State-Trait Anxiety Inventory-scores were correlated with clusters showing significant activation during reward anticipation.
During reward anticipation, we observed significant group differences in ventral striatal (VS) activation: patients with schizophrenia, alcohol dependence, and major depression showed significantly less ventral striatal activation compared to healthy controls. Depressive symptoms correlated with dysfunction in reward anticipation regardless of diagnostic entity. There was no significant correlation between anxiety symptoms and VS functional activation.
Our findings demonstrate a neurobiological dysfunction related to reward prediction that transcended disorder categories and was related to measures of depressed mood. The findings underline the potential of a dimensional approach in psychiatry and strengthen the hypothesis that neurobiological research in psychiatric disorders can be targeted at core mechanisms that are likely to be implicated in a range of clinical entities.
Diffusion of finite-size particles in two-dimensional channels with random wall configurations
(2014)
Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick–Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda [J. Chem. Phys., 2012, 137, 024107].
Zinc deficiency has a fundamental influence on the immune defense, with multiple effects on different immune cells, resulting in a major impairment of human health. Monocytes and macrophages are among the immune cells that are most fundamentally affected by zinc, but the impact of zinc on these cells is still far from being completely understood. Therefore, this study investigates the influence of zinc deficiency on monocytes of healthy human donors. Peripheral blood mononuclear cells, which include monocytes, were cultured under zinc deficient conditions for 3 days. This was achieved by two different methods: by application of the membrane permeable chelator N,N,N0´,N0´-tetrakis-(2-pyridylmethyl)ethylenediamine (TPEN) or by removal of zinc from the culture medium using a CHELEX 100 resin. Subsequently, monocyte functions were analyzed in response to Escherichia coli, Staphylococcus aureus, and Streptococcus pneumoniae. Zinc depletion had differential effects. On the one hand, elimination of bacterial pathogens by phagocytosis and oxidative burst was elevated. On the other hand, the production of the inflammatory cytokines tumor necrosis factor (TNF)-a and interleukin (IL)-6 was reduced. This suggests that monocytes shift from intercellular communication to basic innate defensive functions in response to zinc deficiency. These results were obtained regardless of the method by which zinc deficiency was achieved. However, CHELEX-treated medium strongly augmented cytokine production, independently from its capability for zinc removal. This side-effect severely limits the use of CHELEX for investigating the effects of zinc deficiency on innate immunity.
Norwegen rühmt sich gern seiner „offenen Gesellschaft“: Migranten sind willkommen, vor allem qualifizierte Facharbeiter. Nach den jüngsten Wahlen im Sommer 2013, aus denen die Konservativen als Sieger hervorgingen, könnten nun die Einwanderungsgesetze verschärft werden. Schon jetzt bedient sich Norwegen europäischer Regelungen, die seinem Wunsch nach „effektiver Einwanderung“ entgegenkommen.
Werner Mittenzwei’s article of 1967, the title of which coined the term “Brecht-Lukács-Debatte”, is widely considered as a milestone in the development of East German literary criticism towards an “emancipation” from party politics. By placing Mittenzwei’s contribution in the wider context of discussions about the literature of the GDR, within the SED and the writers’ union as well as at international conferences, this article attempts to trace the emergence of “Umfunktionierung” both as a key term and in its official approval by the party.
Hemolysis, the rupturing of red blood cells, can result from numerous medical conditions (in vivo) or occur after collecting blood specimen or extracting plasma and serum out of whole blood (in vitro). In clinical laboratory practice, hemolysis can be a serious problem due to its potential to bias detection of various analytes or biomarkers. Here we present the first ‘‘mix-and-measure’’ method to assess the degree of hemolysis in biosamples using luminescence spectroscopy. Luminescent terbium complexes (LTC) were studied in the presence of free hemoglobin (Hb) as indicators for hemolysis in TRIS-buffer, and in fresh human plasma with absorption, excitation and emission measurements. Our findings indicate dynamic as well as resonance energy transfer (FRET) between the LTC and the porphyrin ligand of hemoglobin. This transfer leads to a decrease in luminescence intensity and decay time even at nanomolar hemoglobin concentrations either in buffer or plasma. Luminescent terbium complexes are very sensitive to free hemoglobin in buffer and blood plasma. Due to the instant change in luminescence properties of the LTC in presence of Hb it is possible to access the concentration of hemoglobin via spectroscopic methods without incubation time or further treatment of the sample thus enabling a rapid and sensitive detection of hemolysis in clinical diagnostics.
Historiografie und Publizistik haben den Kriegsausbruch von 1914 immer aus unterschiedlichen Blickwinkeln und mit wechselnden Intentionen behandelt. Dabei wurde deutlich, dass sich mit der Überwindung der nationalen Perspektive auf 1914 zugleich auch unser Blick auf die Verantwortlichkeit der einzelnen europäischen Regierungen erweitert hat. Damit ist die Kriegsschuldfrage, die gleich am Anfang der Debatte um 1914 gestanden hatte und gerade nach den Pariser Vorortverträgen instrumentalisiert worden war, eigentlich obsolet geworden und einer Perspektive gewichen, die, frei von tagespolitischen Belastungen, nationalen Feindbildern und Vorurteilen, Schuld und Verantwortung in ihren Verschränkungen mit dem politischen Entscheidungshandeln verdeutlicht und dabei auch die systemischen Voraussetzungen und Folgen in Rechnung stellt.
Based on extensive Monte Carlo simulations and analytical considerations we study the electrostatically driven adsorption of flexible polyelectrolyte chains onto charged Janus nanospheres. These net-neutral colloids are composed of two equally but oppositely charged hemispheres. The critical binding conditions for polyelectrolyte chains are analysed as function of the radius of the Janus particle and its surface charge density, as well as the salt concentration in the ambient solution. Specifically for the adsorption of finite-length polyelectrolyte chains onto Janus nanoparticles, we demonstrate that the critical adsorption conditions drastically differ when the size of the Janus particle or the screening length of the electrolyte are varied. We compare the scaling laws obtained for the adsorption–desorption threshold to the known results for uniformly charged spherical particles, observing significant disparities. We also contrast the changes to the polyelectrolyte chain conformations close to the surface of the Janus nanoparticles as compared to those for simple spherical particles. Finally, we discuss experimentally relevant physico-chemical systems for which our simulations results may become important. In particular, we observe similar trends with polyelectrolyte complexation with oppositely but heterogeneously charged proteins.
Photoinduced excitation energy transfer and accompanying charge separation are elucidated for a supramolecular system of a single fullerene covalently linked to six pyropheophorbide-a dye molecules. Molecular dynamics simulations are performed to gain an atomistic picture of the architecture and the surrounding solvent. Excitation energy transfer among the dye molecules and electron transfer from the excited dyes to the fullerene are described by a mixed quantum–classical version of the Förster rate and the semiclassical Marcus rate, respectively. The mean characteristic time of energy redistribution lies in the range of 10 ps, while electron transfer proceeds within 150 ps. In between, on a 20 to 50 ps time-scale, conformational changes take place in the system. This temporal hierarchy of processes guarantees efficient charge separation, if the structure is exposed to a solvent. The fast energy transfer can adopt the dye excitation to the actual conformation. In this sense, the probability to achieve charge separation is large enough since any dominance of unfavorable conformations that exhibit a large dye–fullerene distance is circumvented. And the slow electron transfer may realize an averaging with respect to different conformations. To confirm the reliability of our computations, ensemble measurements on the charge separation dynamics are simulated and a very good agreement with the experimental data is obtained.
Background
The Amazon molly, Poecilia formosa (Teleostei: Poeciliinae) is an unisexual, all-female species. It evolved through the hybridisation of two closely related sexual species and exhibits clonal reproduction by sperm dependent parthenogenesis (or gynogenesis) where the sperm of a parental species is only used to activate embryogenesis of the apomictic, diploid eggs but does not contribute genetic material to the offspring.
Here we provide and describe the first de novo assembled transcriptome of the Amazon molly in comparison with its maternal ancestor, the Atlantic molly Poecilia mexicana. The transcriptome data were produced through sequencing of single end libraries (100 bp) with the Illumina sequencing technique.
Results
83,504,382 reads for the Amazon molly and 81,625,840 for the Atlantic molly were assembled into 127,283 and 78,961 contigs for the Amazon molly and the Atlantic molly, respectively. 63% resp. 57% of the contigs could be annotated with gene ontology terms after sequence similarity comparisons. Furthermore, we were able to identify genes normally involved in reproduction and especially in meiosis also in the transcriptome dataset of the apomictic reproducing Amazon molly.
Conclusions
We assembled and annotated the transcriptome of a non-model organism, the Amazon molly, without a reference genome (de novo). The obtained dataset is a fundamental resource for future research in functional and expression analysis. Also, the presence of 30 meiosis-specific genes within a species where no meiosis is known to take place is remarkable and raises new questions for future research.
We propose a novel cluster-based reduced-order modelling (CROM) strategy for unsteady flows. CROM combines the cluster analysis pioneered in Gunzburger's group (Burkardt, Gunzburger & Lee, Comput. Meth. Appl. Mech. Engng, vol. 196, 2006a, pp. 337-355) and transition matrix models introduced in fluid dynamics in Eckhardt's group (Schneider, Eckhardt & Vollmer, Phys. Rev. E, vol. 75, 2007, art. 066313). CROM constitutes a potential alternative to POD models and generalises the Ulam-Galerkin method classically used in dynamical systems to determine a finite-rank approximation of the Perron-Frobenius operator. The proposed strategy processes a time-resolved sequence of flow snapshots in two steps. First, the snapshot data are clustered into a small number of representative states, called centroids, in the state space. These centroids partition the state space in complementary non-overlapping regions (centroidal Voronoi cells). Departing from the standard algorithm, the probabilities of the clusters are determined, and the states are sorted by analysis of the transition matrix. Second, the transitions between the states are dynamically modelled using a Markov process. Physical mechanisms are then distilled by a refined analysis of the Markov process, e. g. using finite-time Lyapunov exponent (FTLE) and entropic methods. This CROM framework is applied to the Lorenz attractor (as illustrative example), to velocity fields of the spatially evolving incompressible mixing layer and the three-dimensional turbulent wake of a bluff body. For these examples, CROM is shown to identify non-trivial quasi-attractors and transition processes in an unsupervised manner. CROM has numerous potential applications for the systematic identification of physical mechanisms of complex dynamics, for comparison of flow evolution models, for the identification of precursors to desirable and undesirable events, and for flow control applications exploiting nonlinear actuation dynamics.
claspfolio 2
(2014)
Building on the award-winning, portfolio-based ASP solver claspfolio, we present claspfolio 2, a modular and open solver architecture that integrates several different portfolio-based algorithm selection approaches and techniques. The claspfolio 2 solver framework supports various feature generators, solver selection approaches, solver portfolios, as well as solver-schedule-based pre-solving techniques. The default configuration of claspfolio 2 relies on a light-weight version of the ASP solver clasp to generate static and dynamic instance features. The flexible open design of claspfolio 2 is a distinguishing factor even beyond ASP. As such, it provides a unique framework for comparing and combining existing portfolio-based algorithm selection approaches and techniques in a single, unified framework. Taking advantage of this, we conducted an extensive experimental study to assess the impact of different feature sets, selection approaches and base solver portfolios. In addition to gaining substantial insights into the utility of the various approaches and techniques, we identified a default configuration of claspfolio 2 that achieves substantial performance gains not only over clasp's default configuration and the earlier version of claspfolio, but also over manually tuned configurations of clasp.
Herein, we report the chain-growth tin-free room temperature polymerization method to synthesize n-type perylene diimide-dithiophene-based conjugated polymers (PPDIT2s) suitable for solar cell and transistor applications. The palladium/electron-rich tri-tert-butylphosphine catalyst is effective to enable the chain-growth polymerization of anion-radical monomer Br-TPDIT-Br/Zn to PPDIT2 with a molecular weight up to Mw ≈ 50 kg mol−1 and moderate polydispersity. This is the second example of the polymerization of unusual anion-radical aromatic complexes formed in a reaction of active Zn and electron-deficient diimide-based aryl halides. As such, the discovered polymerization method is not a specific reactivity feature of the naphthalene-diimide derivatives but is rather a general polymerization tool. This is an important finding, given the significantly higher maximum external quantum efficiency that can be reached with PDI-based copolymers (32–45%) in all-polymer solar cells compared to NDI-based materials (15–30%). Our studies revealed that PPDIT2 synthesized by the new method and the previously published polymer prepared by step-growth Stille polycondensation show similar electron mobility and all-polymer solar cell performance. At the same time, the polymerization reported herein has several technological advantages as it proceeds relatively fast at room temperature and does not involve toxic tin-based compounds. Because several chain-growth polymerization reactions are well-suited for the preparation of well-defined multi-functional polymer architectures, the next target is to explore the utility of the discovered polymerization in the synthesis of end-functionalized polymers and block copolymers. Such materials would be helpful to improve the nanoscale morphology of polymer blends in all-polymer solar cells.
Catalytic bio–chemo and bio–bio tandem oxidation reactions for amide and carboxylic acid synthesis
(2014)
A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or CuI(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields.
Recently, C K-edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of graphite (HOPG) surfaces have been measured for the pristine material, and for HOPG treated with either bromine or krypton plasmas (Lippitz et al., Surf. Sci., 2013, 611, L1). Changes of the NEXAFS spectra characteristic for physical (krypton) and/or chemical/physical modifications of the surface (bromine) upon plasma treatment were observed. Their molecular origin, however, remained elusive. In this work we study by density functional theory, the effects of selected point and line defects as well as chemical modifications on NEXAFS carbon K-edge spectra of single graphene layers. For Br-treated surfaces, also Br 3d X-ray Photoelectron Spectra (XPS) are simulated by a cluster approach, to identify possible chemical modifications. We observe that some of the defects related to plasma treatment lead to characteristic changes of NEXAFS spectra, similar to those in experiment. Theory provides possible microscopic origins for these changes.
Enthüllungen über groß angelegte NSA-Lauschangriffe auf die Bundesrepublik, die auch vor dem Mobiltelefon der Bundeskanzlerin nicht haltmachten, haben mit neuer Intensität nicht nur die Frage nach dem deutsch-amerikanischen Verhältnis auf die Tagesordnung gesetzt. Bedeutet diese Massenspionage, dass Grundrechte in Deutschland von auswärtigen Diensten umstandslos außer Kraft gesetzt werden können? Oder ist sie der Vorbote eines aufziehenden Hegemonialkonflikts zwischen der EU und den USA?
Ausências Brasil
(2014)
Von der Militärdiktatur ermordet und spurlos verschwunden – diese Ausstellung greift zurück auf Fotoalben der Familienangehörigen von Brasilianern, die der systematischen Repression, Folter und Verschleppung der brasilianischen Militärdiktatur (1964–1985) zum Opfer gefallen sind: Arbeiter, Stadtguerilleros, Studenten, Akademiker, ganze Familien.