Dynamic restructuring drives catalytic activity on nanoporous gold-silver alloy catalysts.

Bimetallic, nanostructured materials hold promise for improving catalyst activity and selectivity, yet little is known about the dynamic compositional and structural changes that these systems undergo during pretreatment that leads to efficient catalyst function. Here we use ozone-activated silver-gold alloys in the form of nanoporous gold as a case study to demonstrate the dynamic behaviour of bimetallic systems during activation to produce a functioning catalyst. We show that it is these dynamic changes that give rise to the observed catalytic activity. Advanced in situ electron microscopy and X-ray photoelectron spectroscopy are used to demonstrate that major restructuring and compositional changes occur along the path to catalytic function for selective alcohol oxidation. Transient kinetic measurements correlate the restructuring to three types of oxygen on the surface. The direct influence of changes in surface silver concentration and restructuring at the nanoscale on oxidation activity is demonstrated. Our results demonstrate that characterization of these dynamic changes is necessary to unlock the full potential of bimetallic catalytic materials.

Selective Irreversible Inhibition of Neuronal and Inducible Nitric-oxide Synthase in the Combined Presence of Hydrogen Sulfide and Nitric Oxide.

Citrulline formation by both human neuronal nitric-oxide synthase (nNOS) and mouse macrophage inducible NOS was inhibited by the hydrogen sulfide (H2S) donor Na2S with IC50 values of ∼2.4·10(-5) and ∼7.9·10(-5) m, respectively, whereas human endothelial NOS was hardly affected at all. Inhibition of nNOS was not affected by the concentrations of l-arginine (Arg), NADPH, FAD, FMN, tetrahydrobiopterin (BH4), and calmodulin, indicating that H2S does not interfere with substrate or cofactor binding. The IC50 decreased to ∼1.5·10(-5) m at pH 6.0 and increased to ∼8.3·10(-5) m at pH 8.0. Preincubation of concentrated nNOS with H2S under turnover conditions decreased activity after dilution by ∼70%, suggesting irreversible inhibition. However, when calmodulin was omitted during preincubation, activity was not affected, suggesting that irreversible inhibition requires both H2S and NO. Likewise, NADPH oxidation was inhibited with an IC50 of ∼1.9·10(-5) m in the presence of Arg and BH4 but exhibited much higher IC50 values (∼1.0-6.1·10(-4) m) when Arg and/or BH4 was omitted. Moreover, the relatively weak inhibition of nNOS by Na2S in the absence of Arg and/or BH4 was markedly potentiated by the NO donor 1-(hydroxy-NNO-azoxy)-l-proline, disodium salt (IC50 ∼ 1.3-2.0·10(-5) m). These results suggest that nNOS and inducible NOS but not endothelial NOS are irreversibly inhibited by H2S/NO at modest concentrations of H2S in a reaction that may allow feedback inhibition of NO production under conditions of excessive NO/H2S formation.

Recycling of CO2: Probing the Chemical State of the Ni(111) Surface during the Methanation Reaction with Ambient-Pressure X-Ray Photoelectron Spectroscopy.

Using ambient-pressure X-ray photoelectron spectroscopy (AP-XPS), we studied the adsorption and reactions of CO2 and CO2 + H2 on the Ni(111) surface to identify the surface chemical state and the nature of the adsorbed species during the methanation reaction. In 200 mTorr CO2, we found that NiO is formed from CO2 dissociation into CO and atomic oxygen. Additionally, carbonate (CO32-) is present on the surface from further reaction of CO2 with NiO. The addition of H2 into the reaction environment leads to reduction of NiO and the disappearance of CO32-. At temperatures >160 °C, CO adsorbed on hollow sites, and atomic carbon and OH species are present on the surface. We conclude that the methanation reaction proceeds via dissociation of CO2, followed by reduction of CO to atomic carbon and its hydrogenation to methane.

Catalyst Chemical State during CO Oxidation Reaction on Cu(111) Studied with Ambient-Pressure X-ray Photoelectron Spectroscopy and Near Edge X-ray Adsorption Fine Structure Spectroscopy.

The chemical structure of a Cu(111) model catalyst during the CO oxidation reaction in the CO+O2 pressure range of 10-300 mTorr at 298-413 K was studied in situ using surface sensitive X-ray photoelectron and adsorption spectroscopy techniques [X-ray photoelectron spectroscopy (XPS) and near edge X-ray adsorption fine structure spectroscopy (NEXAFS)]. For O2:CO partial pressure ratios below 1:3, the surface is covered by chemisorbed O and by a thin (∼1 nm) Cu2O layer, which covers completely the surface for ratios above 1:3 between 333 and 413 K. The Cu2O film increases in thickness and exceeds the escape depth (∼3-4 nm) of the XPS and NEXAFS photoelectrons used for analysis at 413 K. No CuO formation was detected under the reaction conditions used in this work. The main reaction intermediate was found to be CO2(δ-), with a coverage that correlates with the amount of Cu2O, suggesting that this phase is the most active for CO oxidation.

Forecasted coral reef decline in marine biodiversity hotspots under climate change.

Coral bleaching events threaten coral reef habitats globally and cause severe declines of local biodiversity and productivity. Related to high sea surface temperatures (SST), bleaching events are expected to increase as a consequence of future global warming. However, response to climate change is still uncertain as future low-latitude climatic conditions have no present-day analogue. Sea surface temperatures during the Eocene epoch were warmer than forecasted changes for the coming century, and distributions of corals during the Eocene may help to inform models forecasting the future of coral reefs. We coupled contemporary and Eocene coral occurrences with information on their respective climatic conditions to model the thermal niche of coral reefs and its potential response to projected climate change. We found that under the RCP8.5 climate change scenario, the global suitability for coral reefs may increase up to 16% by 2100, mostly due to improved suitability of higher latitudes. In contrast, in its current range, coral reef suitability may decrease up to 46% by 2100. Reduction in thermal suitability will be most severe in biodiversity hotspots, especially in the Indo-Australian Archipelago. Our results suggest that many contemporary hotspots for coral reefs, including those that have been refugia in the past, spatially mismatch with future suitable areas for coral reefs posing challenges to conservation actions under climate change.

The impact of steam on the electronic structure of the selective propane oxidation catalyst MoVTeNb oxide (orthorhombic M1 phase).

The selective propane oxidation catalyst MoVTeNb oxide M1 was investigated by microwave conductivity, synchrotron X-ray photoelectron, soft X-ray absorption and resonant photoelectron spectroscopy under reaction conditions to identify the influence of steam on the electronic bulk and surface properties. Steam significantly increases both the conversion of propane and the selectivity to the target product acrylic acid. The increased catalytic performance comes along with a decreased conductivity, a modification of the surface chemical and electronic structure with an enrichment of covalently bonded V(5+) species to the extent of Mo(6+), a decreased work function and hence polarity of the surface and a modified valence band structure. The higher degree of covalency in metal oxide bonds affects the mobility of the free charge carriers, and hence explains the decrease of the conductivity with steam. Furthermore we could prove that a subsurface space charge region depleted in electrons and thus an upward bending of the electronic band structure are induced by the reaction mixture, which is however not dependent on the steam content.

lin-28 controls the succession of cell fate choices via two distinct activities.

lin-28 is a conserved regulator of cell fate succession in animals. In Caenorhabditis elegans, it is a component of the heterochronic gene pathway that governs larval developmental timing, while its vertebrate homologs promote pluripotency and control differentiation in diverse tissues. The RNA binding protein encoded by lin-28 can directly inhibit let-7 microRNA processing by a novel mechanism that is conserved from worms to humans. We found that C. elegans LIN-28 protein can interact with four distinct let-7 family pre-microRNAs, but in vivo inhibits the premature accumulation of only let-7. Surprisingly, however, lin-28 does not require let-7 or its relatives for its characteristic promotion of second larval stage cell fates. In other words, we find that the premature accumulation of mature let-7 does not account for lin-28's precocious phenotype. To explain let-7's role in lin-28 activity, we provide evidence that lin-28 acts in two steps: first, the let-7-independent positive regulation of hbl-1 through its 3'UTR to control L2 stage-specific cell fates; and second, a let-7-dependent step that controls subsequent fates via repression of lin-41. Our evidence also indicates that let-7 functions one stage earlier in C. elegans development than previously thought. Importantly, lin-28's two-step mechanism resembles that of the heterochronic gene lin-14, and the overlap of their activities suggests a clockwork mechanism for developmental timing. Furthermore, this model explains the previous observation that mammalian Lin28 has two genetically separable activities. Thus, lin-28's two-step mechanism may be an essential feature of its evolutionarily conserved role in cell fate succession.

The electronic factor in alkane oxidation catalysis.

This article addresses the fundamental question of whether concepts from semiconductor physics can be applied to describe the working mode of heterogeneous oxidation catalysts and whether they can be even used to discriminate between selective and unselective reaction pathways. Near-ambient-pressure X-ray photoelectron spectroscopy was applied to the oxidation of n-butane to maleic anhydride on the highly selective catalyst vanadyl pyrophosphate and the moderately selective MoVTeNbO(x) M1 phase. The catalysts were found to act like semiconducting gas sensors with a dynamic charge transfer between the bulk and the surface, as indicated by the gas-phase-dependent response of the work function, electron affinity, and the surface potential barrier. In contrast, only a minor influence of the gas phase on the semiconducting properties and hence no dynamic surface potential barrier was monitored for the total oxidation catalyst V2O5. The surface potential barrier is hence suggested as descriptor for selective catalysts.

Interaction between neuronal nitric-oxide synthase and tetrahydrobiopterin revisited: studies on the nature and mechanism of tight pterin binding.

Recombinant neuronal nitric-oxide synthase (nNOS) expressed in baculovirus-infected Sf9 cells contains approximately 1 equiv of tightly bound tetrahydrobiopterin (BH4) per dimer and binds a second equivalent with a dissociation constant in the 10(-7)-10(-6) M range. Less is known about the pterin-binding properties of nNOS originating from expression systems such as Escherichia coli that do not produce BH4. We determined the binding properties of E. coli-expressed nNOS for BH4 and several inhibitory pterins by monitoring their effects on enzyme activity. E. coli-expressed nNOS as isolated was activated by BH4 monophasically with EC50 ≈ 2 × 10(-7) M, demonstrating a lack of tight pterin binding. However, overnight incubation with BH4 resulted in tight binding of one BH4 per dimer, yielding an enzyme that resembled Sf9-expressed nNOS. Tight pterin binding was also induced by preincubation with 4-amino-tetrahydrobiopterin, but not by 7,8-dihydrobiopterin or 4-amino-dihydrobiopterin, suggesting that tight-binding site formation requires preincubation with a fully reduced pteridine. Kinetic experiments showed that tight-binding site formation takes approximately 10 min with 1 µM BH4 (2 min with 1 µM 4-amino-BH4) at 4 °C. Anaerobic preincubation experiments demonstrated that O2 is not involved in the process. Gel electrophoretic studies suggest that tight-binding site formation is accompanied by an increase in the strength of the NOS dimer. We propose that incubation of pterin-free nNOS with BH4 creates one tight pterin-binding site per dimer, leaving the other site unaffected, in a reaction that involves redox chemistry.

Diffusion restriction of the optic nerve in patients with acute visual deficit.

PURPOSE: Diffusion magnetic resonance imaging (MRI) is commonly used in acute stroke, but not considered diagnostic in ischemic optic neuropathy. This study evaluates the presence of diffusion restriction in patients with acute visual loss by analyzing diffusion-weighted images (DWI). MATERIALS AND METHODS: A retrospective study of all patients who clinically presented with acute visual loss and who underwent MRI with DWI between January 2011 and May 2012 were evaluated. Patients with suspected brainstem ischemia were used as a control group. Two neuroradiologists evaluated the DWI for the presence of diffusion restriction within the optic nerve. RESULTS: In all, 34 patients with acute visual deficit and 32 controls were evaluated. In all five cases of acute optic ischemia, diffusion restriction with reduced apparent diffusion coefficient was present. In 2/25 patients with clinically defined optic neuritis, a diffusion restriction was present. No diffusion restriction was seen in the control cases or in cases with other causes for an acute visual deficit. CONCLUSION: DWI can identify ischemic lesions of the optic nerve. As in acute multiple sclerosis lesions, optic neuritis can also present in rare circumstances with diffusion restriction and can therefore not be ruled out solely by DWI MRI.

LIN28 alters cell fate succession and acts independently of the let-7 microRNA during neurogliogenesis in vitro.

LIN28 is an RNA-binding protein that is expressed in many developing tissues. It can block let-7 (Mirlet7) microRNA processing and help promote pluripotency. We have observed LIN28 expression in the developing mouse neural tube, colocalizing with SOX2, suggesting a role in neural development. To better understand its normal developmental function, we investigated LIN28 activity during neurogliogenesis in vitro, where the succession of neuronal to glial cell fates occurs as it does in vivo. LIN28 expression was high in undifferentiated cells, and was downregulated rapidly upon differentiation. Constitutive LIN28 expression caused a complete block of gliogenesis and an increase in neurogenesis. LIN28 expression was compatible with neuronal differentiation and did not increase proliferation. LIN28 caused significant changes in gene expression prior to any effect on let-7, notably on Igf2. Furthermore, a mutant LIN28 that permitted let-7 accumulation was still able to completely block gliogenesis. Thus, at least two biological activities of LIN28 are genetically separable and might involve distinct mechanisms. LIN28 can differentially promote and inhibit specific fates and does not function exclusively by blocking let-7 family microRNAs. Importantly, the role of LIN28 in cell fate succession in vertebrate cells is analogous to its activity as a developmental timing regulator in C. elegans.

Missense variant interaction scanning reveals a critical role of the FERM domain for tumor suppressor protein NF2 conformation and function.

NF2 (moesin-ezrin-radixin-like [MERLIN] tumor suppressor) is frequently inactivated in cancer, where its NF2 tumor suppressor functionality is tightly coupled to protein conformation. How NF2 conformation is regulated and how NF2 conformation influences tumor suppressor activity is a largely open question. Here, we systematically characterized three NF2 conformation-dependent protein interactions utilizing deep mutational scanning interaction perturbation analyses. We identified two regions in NF2 with clustered mutations which affected conformation-dependent protein interactions. NF2 variants in the F2-F3 subdomain and the α3H helix region substantially modulated NF2 conformation and homomerization. Mutations in the F2-F3 subdomain altered proliferation in three cell lines and matched patterns of disease mutations in NF2 related-schwannomatosis. This study highlights the power of systematic mutational interaction perturbation analysis to identify missense variants impacting NF2 conformation and provides insight into NF2 tumor suppressor function.

IGF1R Inhibition Enhances the Therapeutic Effects of Gq/11 Inhibition in Metastatic Uveal Melanoma Progression.

Uveal melanoma (UM) is the most common intraocular tumor in adults, and up to 50% of patients develop metastatic disease, which remains uncurable. Because patients with metastatic UM have an average survival of less than 1 year after diagnosis, there is an urgent need to develop new treatment strategies. Although activating mutations in Gαq or Gα11 proteins are major drivers of pathogenesis, the therapeutic intervention of downstream Gαq/11 targets has been unsuccessful in treating UM, possibly due to alternative signaling pathways and/or resistance mechanisms. Activation of the insulin-like growth factor 1 (IGF1) signaling pathway promotes cell growth, metastasis, and drug resistance in many types of cancers, including UM, where expression of the IGF1 receptor (IGF1R) correlates with a poor prognosis. In this article, we show that direct inhibition of Gαq/11 by the cyclic depsipeptide YM-254890 in combination with inhibition of IGF1R by linsitinib cooperatively inhibits downstream signaling and proliferation of UM cells. We further demonstrate that a 2-week combination treatment of 0.3 to 0.4 mg/kg of YM-254890 administered by intraperitoneal injection and 25 to 40 mg/kg linsitinib administered by oral gavage effectively inhibits the growth of metastatic UM tumors in immunodeficient NOD scid gamma (NSG) mice and identifies the IGF1 pathway as a potential resistance mechanism in response to Gαq/11 inhibition in UM. These data suggest that the combination of Gαq/11 and IGF1R inhibition provides a promising therapeutic strategy to treat metastatic UM.

BarMap: RNA folding on dynamic energy landscapes.

Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyze the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on individual landscapes and to model external triggers and environmental changes as small but discrete changes in the landscapes. A "barmap" links macrostates of temporally adjacent landscapes and defines the transfer of population densities from one "snapshot" to the next. Implemented in the BarMap software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many nonstationary scenarios, including temperature changes, cotranscriptional folding, refolding in consequence to degradation, and mechanically constrained kinetics, as in the case of the translocation of a polymer through a pore.

Epitaxial III-V films and surfaces for photoelectrocatalysis.

Efficient photoelectrochemical devices for water splitting benefit from the highest material quality and dedicated surface preparation achieved by epitaxial growth. InP(100)-based half-cells show significant solar-to-hydrogen efficiencies, but require a bias due to insufficient voltage. Tandem absorber structures may provide both adequate potential and efficient utilization of the solar spectrum. We propose epitaxial dilute nitride GaPNAs photocathodes on Si(100) substrates to combine close-to-optimum limiting efficiency, lattice-matched growth, and established surface preparation. Prior to a discussion of the challenging III-V/Si(100) heterojunction, we describe the closely related epitaxial preparation of InP(100) surfaces and its beneficial impact on photoelectrochemical water-splitting performance. Analogies and specific differences to GaP(100) surfaces are discussed based on in situ reflectance anisotropy and on two-photon photoemission results. Preliminary experiments regarding GaP/Si(100) photoelectrochemistry and dilute nitride GaPN heteroepitaxy on Si(100) confirm the potential of the GaPNAs/Si tandem absorber structure for future water-splitting devices.

Towards Modeling Visualization Processes as Dynamic Bayesian Networks.

Visualization designs typically need to be evaluated with user studies, because their suitability for a particular task is hard to predict. What the field of visualization is currently lacking are theories and models that can be used to explain why certain designs work and others do not. This paper outlines a general framework for modeling visualization processes that can serve as the first step towards such a theory. It surveys related research in mathematical and computational psychology and argues for the use of dynamic Bayesian networks to describe these time-dependent, probabilistic processes. It is discussed how these models could be used to aid in design evaluation. The development of concrete models will be a long process. Thus, the paper outlines a research program sketching how to develop prototypes and their extensions from existing models, controlled experiments, and observational studies.

Visualization of graph products.

Graphs are a versatile structure and abstraction for binary relationships between objects. To gain insight into such relationships, their corresponding graph can be visualized. In the past, many classes of graphs have been defined, e.g. trees, planar graphs, directed acyclic graphs, and visualization algorithms were proposed for these classes. Although many graphs may only be classified as "general" graphs, they can contain substructures that belong to a certain class. Archambault proposed the TopoLayout framework: rather than draw any arbitrary graph using one method, split the graph into components that are homogeneous with respect to one graph class and then draw each component with an algorithm best suited for this class. Graph products constitute a class that arises frequently in graph theory, but for which no visualization algorithm has been proposed until now. In this paper, we present an algorithm for drawing graph products and the aesthetic criterion graph product's drawings are subject to. We show that the popular High-Dimensional Embedder approach applied to cartesian products already respects this aestetic criterion, but has disadvantages. We also present how our method is integrated as a new component into the TopoLayout framework. Our implementation is used for further research of graph products in a biological context.

Modeling How Humans Judge Dot-Label Relations in Point Cloud Visualizations.

When point clouds are labeled in information visualization applications, sophisticated guidelines as in cartography do not yet exist. Existing naive strategies may mislead as to which points belong to which label. To inform improved strategies, we studied factors influencing this phenomenon. We derived a class of labeled point cloud representations from existing applications and we defined different models predicting how humans interpret such complex representations, focusing on their geometric properties. We conducted an empirical study, in which participants had to relate dots to labels in order to evaluate how well our models predict. Our results indicate that presence of point clusters, label size, and angle to the label have an effect on participants' judgment as well as that the distance measure types considered perform differently discouraging the use of label centers as reference points.

Influence of Steam on a Vanadyl Pyrophosphate Catalyst During Propane Oxidation.

We have investigated electronic and catalytic modifications of the p-type semiconducting selective oxidation catalyst vanadyl pyrophosphate (VPP) for propane oxidation in the presence and absence of steam. Steam changes propane conversion only slightly, but increases the selectivity toward oxygenates (acrylic acid, acetic acid) and the olefin propylene resulting in reduced selectivity of the undesired total oxidation products CO and CO2. Contact-free in operando microwave conductivity measurements at 0.1 MPa revealed that the modified catalytic performance is accompanied by a reduced electrical conductivity. Surface sensitive near-ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) and X-ray absorption spectroscopy (XAS) measurements at 25 Pa showed that steam depletes the topmost surface of VPP in phosphorus and enhances the average vanadium oxidation state slightly. These findings are accompanied by a decreased work function, but no detectable shift of the valence band edge is observed. Thus, the chemical surface modification changes the surface dipole but leaves the barrier height of the surface induced space charge layer basically unaffected. Hence, we conclude that steam does not affect the electron hole concentration (majority charge carriers) and hence the oxygen vacancy concentration. Therefore, the reduced conductivity can be understood in terms of charge carrier mobility changes, which may affect the selectivity of VPP toward oxygenates with steam. In addition, the modification of local properties, such as the concentration of acid sites as well as the nature and number of adsorption sites may have an impact on the catalytic properties.

Structure of the Clean and Oxygen-Covered Cu(100) Surface at Room Temperature in the Presence of Methanol Vapor in the 10-200 mTorr Pressure Range.

Using ambient pressure X-ray photoelectron spectroscopy (APXPS) and high pressure scanning tunneling microscopy (HPSTM), we show that in equilibrium with 0.01-0.2 Torr of methanol vapor, at room temperature, the Cu(100) surface is covered with methoxy species forming a c(2 × 2) overlayer structure. In contrast, no methoxy is formed if the surface is saturated with an ordered oxygen layer, even when the methanol pressure is 0.2 Torr. At oxygen coverages below saturation, methanol dissociates and reacts with the atomic oxygen, producing methoxy and formate on the surface, and formaldehyde that desorbs to the gas phase. Unlike the case of pure carbon monoxide and carbon dioxide, methanol does not induce the restructuring of the Cu(100) surface. These results provide insight into catalytic anhydrous production of aldehydes.