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.

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.

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.

Interaction modulation through arrays of clustered methyl-arginine protein modifications.

Systematic analysis of human arginine methylation identifies two distinct signaling modes; either isolated modifications akin to canonical post-translational modification regulation, or clustered arrays within disordered protein sequence. Hundreds of proteins contain these methyl-arginine arrays and are more prone to accumulate mutations and more tightly expression-regulated than dispersed methylation targets. Arginines within an array in the highly methylated RNA-binding protein synaptotagmin binding cytoplasmic RNA interacting protein (SYNCRIP) were experimentally shown to function in concert, providing a tunable protein interaction interface. Quantitative immunoprecipitation assays defined two distinct cumulative binding mechanisms operating across 18 proximal arginine-glycine (RG) motifs in SYNCRIP. Functional binding to the methyltransferase PRMT1 was promoted by continual arginine stretches, whereas interaction with the methyl-binding protein SMN1 was arginine content-dependent irrespective of linear position within the unstructured region. This study highlights how highly repetitive modifiable amino acid arrays in low structural complexity regions can provide regulatory platforms, with SYNCRIP as an extreme example how arginine methylation leverages these disordered sequences to mediate cellular interactions.

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.

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.

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.

Plate tectonics drive tropical reef biodiversity dynamics.

The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics.

Augmentation of phosphate-induced osteo-/chondrogenic transformation of vascular smooth muscle cells by homoarginine.

AIMS: Reduced homoarginine plasma levels are associated with unfavourable cardiovascular outcome in chronic kidney disease (CKD). Cardiovascular events in CKD are fostered by vascular calcification, an active process promoted by hyperphosphatemia and involving osteo-/chondrogenic transformation of vascular smooth muscle cells (VSMCs). The present study explored the effect of homoarginine on phosphate-induced osteo-/chondrogenic signalling and vascular calcification. METHODS AND RESULTS: Experiments were performed in hyperphosphatemic klotho-hypomorphic mice (kl/kl), in subtotal nephrectomy and vitamin D3-overload mouse calcification models and in primary human aortic smooth muscle cells (HAoSMCs). As a result, plasma homoarginine levels were lower in kl/kl mice than in wild-type mice and in both genotypes significantly increased by lifelong treatment with homoarginine. Surprisingly, homoarginine treatment of kl/kl mice and of mice with renal failure after subtotal nephrectomy augmented vascular calcification and enhanced the transcript levels of plasminogen activator inhibitor 1 (Pai1) and of osteogenic markers Msx2, Cbfa1, and Alpl. Similarly, homoarginine treatment of HAoSMCs increased phosphate-induced calcium deposition, ALP activity, as well as PAI1, MSX2, CBFA1, and ALPL mRNA levels. Homoarginine alone up-regulated osteo-/chondrogenic signalling and indicators of oxidative stress in HAoSMCs. Furthermore, homoarginine reduced citrulline formation from arginine by nitric oxide (NO) synthase (NOS) isoforms. NO formation by NOS was reduced when using homoarginine as a substrate instead of arginine. The osteoinductive effects of homoarginine were mimicked by NOS inhibitor L-NAME and abolished by additional treatment with the NO donors DETA-NONOate and PAPA-NONOate or the antioxidants TEMPOL and TIRON. Furthermore, homoarginine augmented vascular calcification and aortic osteo-/chondrogenic signalling in mice after vitamin D3-overload, effects reversed by the NO donor molsidomine. CONCLUSION: Homoarginine augments osteo-/chondrogenic transformation of VSMCs and vascular calcification, effects involving impaired NO formation from homoarginine.

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.

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.

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.

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.

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.

Aerobic nitric oxide-induced thiol nitrosation in the presence and absence of magnesium cations.

Although different routes for the S-nitrosation of cysteinyl residues have been proposed, the main in vivo pathway is unknown. We recently demonstrated that direct (as opposed to autoxidation-mediated) aerobic nitrosation of glutathione is surprisingly efficient, especially in the presence of Mg(2+). In the present study we investigated this reaction in greater detail. From the rates of NO decay and the yields of nitrosoglutathione (GSNO) we estimated values for the apparent rate constants of 8.9 ± 0.4 and 0.55 ± 0.06 M(-1)s(-1) in the presence and absence of Mg(2+). The maximum yield of GSNO was close to 100% in the presence of Mg(2+) but only about half as high in its absence. From this observation we conclude that, in the absence of Mg(2+), nitrosation starts by formation of a complex between NO and O2, which then reacts with the thiol. Omission of superoxide dismutase (SOD) reduced by half the GSNO yield in the absence of Mg(2+), demonstrating O2(-) formation. The reaction in the presence of Mg(2+) seems to involve formation of a Mg(2+)•glutathione (GSH) complex. SOD did not affect Mg(2+)-stimulated nitrosation, suggesting that no O2(-) is formed in that reaction. Replacing GSH with other thiols revealed that reaction rates increased with the pKa of the thiol, suggesting that the nucleophilicity of the thiol is crucial for the reaction, but that the thiol need not be deprotonated. We propose that in cells Mg(2+)-stimulated NO/O2-induced nitrosothiol formation may be a physiologically relevant reaction.

Rift migration explains continental margin asymmetry and crustal hyper-extension.

When continents break apart, continental crust and lithosphere are thinned until break-up is achieved and an oceanic basin is formed. The most remarkable and least understood structures associated with this process are up to 200 km wide areas of hyper-extended continental crust, which are partitioned between conjugate margins with pronounced asymmetry. Here we show, using high-resolution thermo-mechanical modelling, that hyper-extended crust and margin asymmetry are produced by steady state rift migration. We demonstrate that rift migration is accomplished by sequential, oceanward-younging, upper crustal faults, and is balanced through lower crustal flow. Constraining our model with a new South Atlantic plate reconstruction, we demonstrate that larger extension velocities may account for southward increasing width and asymmetry of these conjugate magma-poor margins. Our model challenges conventional ideas of rifted margin evolution, as it implies that during rift migration large amounts of material are transferred from one side of the rift zone to the other.

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.

The pupil can control an artificial lens intuitively.

PURPOSE: After cataract surgery, the ability to accommodate is lost. For this reason, a mechatronic IOL is being developed at the moment: The Artificial Accommodation System. This device requires an easily measureable indicator of the distance of the observed object to determine the demand of accommodation. As the pupil constricts with near vision, pupil size might be such an indicator. Our research focused on whether the pupil can control an artificial lens. METHODS: A study with 14 healthy subjects aged between 24 and 64 years was conducted. An artificial lens with variable refractive power was mounted in front of one eye. In this eye, natural accommodation was greatly reduced or absent due to presbyopia, pseudophakia, or iatrogenic cycloplegia. The lens' refractive power was changed in a computer-controlled manner depending on changes in the pupil diameter of the second eye, which could not see the fixation stimulus. The subject's task was to get a clear focused image of the target in different distances. RESULTS: The lens can be controlled by the pupil intuitively (P < 1.8 × 10(-18)). Without prior knowledge, 11/14 subjects passed the first trial, and 31/41 trials were successful. Only one subject was not able to control the lens at all. Most subjects comprehended instantly how to use the unfamiliar lens control to bring a target into focus. CONCLUSIONS: This study emphasizes the plasticity of the visual control system. Positioning accuracy was acceptable, but the control must be optimized to facilitate maintaining a defined refractive power.