On the interaction of Mg with the (111) and (110) surfaces of ceria

The catalytic activity of cerium dioxide can be modified by deposition of alkaline earth oxide layers or nanoparticles or by substitutional doping of metal cations at the Ce site in ceria. In order to understand the effect of Mg oxide deposition and doping, a combination of experiment and first principles simulations is a powerful tool. In this paper, we examine the interaction of Mg with the ceria (111) surface using both angle resolved X-ray (ARXPS) and resonant (RPES) photoelectron spectroscopy measurements and density functional theory (DFT) corrected for on-site Coulomb interactions (DFT + U). With DFT + U, we also examine the interaction of Mg with the ceria (110) surface. The experiments show that upon deposition of Mg, Ce ions are reduced to Ce3+, while Mg is oxidised. When Mg is incorporated into ceria, no reduced Ce3+ ions are found and oxygen vacancies are present. The DFT + U simulations show that each Mg that is introduced leads to formation of two reduced Ce3+ ions. When Mg is incorporated at a Ce site in the (111) surface, one oxygen vacancy is formed for each Mg to compensate the different valencies, so that all Ce ions are oxidised. The behaviour of Mg upon interaction with the (110) surface is the same as with the (111) surface. The combined results provide a basis for deeper insights into the catalytic behaviour of ceria-based mixed oxide catalysts

Genetic Modifier Screens Reveal New Components that Interact with the Drosophila Dystroglycan-Dystrophin Complex

The Dystroglycan-Dystrophin (Dg-Dys) complex has a capacity to transmit information from the extracellular matrix to the cytoskeleton inside the cell. It is proposed that this interaction is under tight regulation; however the signaling/regulatory components of Dg-Dys complex remain elusive. Understanding the regulation of the complex is critical since defects in this complex cause muscular dystrophy in humans. To reveal new regulators of the Dg-Dys complex, we used a model organism Drosophila melanogaster and performed genetic interaction screens to identify modifiers of Dg and Dys mutants in Drosophila wing veins. These mutant screens revealed that the Dg-Dys complex interacts with genes involved in muscle function and components of Notch, TGF-β and EGFR signaling pathways. In addition, components of pathways that are required for cellular and/or axonal migration through cytoskeletal regulation, such as Semaphorin-Plexin, Frazzled-Netrin and Slit-Robo pathways show interactions with Dys and/or Dg. These data suggest that the Dg-Dys complex and the other pathways regulating extracellular information transfer to the cytoskeletal dynamics are more intercalated than previously thought

Role of Solvent and Dendritic Architecture on the Redox Core Encapsulation

Dendrimers with redox cores can accept, donate, and/or store electrons and are used in nanoscale devices like artificial receptors, magnetic resonance imaging, sensors, light harvesting antennae, and electrical switches. However, the dendrimer molecular architectures can significantly alter the encapsulation of the redox core and charge transfer pathways, thereby changing the electron transfer rates. In this study, we used molecular dynamics simulations to investigate the role of solvent and peripheral groups on molecular structure and core encapsulation of iron–sulfur G2-benzyl ether dendrimers in polar and nonpolar solvent. We found that the dendrimer branches collapse in water and swell in chloroform. The presence of the long hydrophobic alkyl groups at the periphery deters the encapsulation of the core in water which may cause an increase in electron transfer rate. However, in chloroform, the dendrimer branches remain in the extended form, which leads to an increased radius of gyration. Our results suggest that peripheral alkyl chains in dendrimers cause steric hindrance, which prevents branches from back folding in chloroform solvent, but in water it reverses the trend. Overall, the presence of a hydrophobic interior and hydrophilic periphery in a dendrimer improves core encapsulation in water while hindering encapsulation in chloroform

Molecular Engineering of the Kinetic Barrier in Seeded Supramolecular Polymerization

Seeded supramolecular polymerization (SSP) is a method that enables the controlled synthesis of supramolecular structures. SSP often relies on structures that are capable of self-assembly by interconverting between intramolecular and intermolecular modes of hydrogen bonding, characterized by a given kinetic barrier that is typically low. The control of the polymerization process is thus limited by the propensity of the hydrogen bonds to interconvert between the intramolecular and intermolecular modes of binding. Here, we report on an engineering of the polymerization kinetic barriers by sophisticated molecular design of the building blocks involved in such SSP processes. Our designs include two types of intramolecular hydrogen-bonded rings: on one hand, a central triazine tricarboxamide moiety that prevents self-assembly due to its stable intramolecular hydrogen bonds and on the other hand, three peripheral amide groups that promote self-assembly due to their stable intermolecular hydrogen bonds. We report a series of molecules with increasing bulkiness of the peripheral side chains exhibiting increasing kinetic stability in the monomeric form. Owing to the relative height of the barrier, we were able to observe that the rate constant of seeding is not proportional to the concentration of the seeds used. Based on that, we proposed a new kinetic model in which the rate-determining step is the activation of the monomer, and we provide the detailed energy landscape of the supramolecular polymerization process. Finally, we investigated the hetero-seeding of the building blocks that shows either inhibition or triggering of the polymerization

Cathepsin L Stabilizes the Histone Modification Landscape on the Y Chromosome and Pericentromeric Heterochromatin

Posttranslational histone modifications and histone variants form a unique epigenetic landscape on mammalian chromosomes where the principal epigenetic heterochromatin markers, trimethylated histone H3(K9) and the histone H2A.Z, are inversely localized in relation to each other. Trimethylated H3(K9) marks pericentromeric constitutive heterochromatin and the male Y chromosome, while H2A.Z is dramatically reduced at these chromosomal locations. Inactivation of a lysosomal and nuclear protease, cathepsin L, causes a global redistribution of epigenetic markers. In cathepsin L knockout cells, the levels of trimethylated H3(K9) decrease dramatically, concomitant with its relocation away from heterochromatin, and H2A.Z becomes enriched at pericentromeric heterochromatin and the Y chromosome. This change is also associated with global relocation of heterochromatin protein HP1 and histone H3 methyltransferase Suv39h1 away from constitutive heterochromatin; however, it does not affect DNA methylation or chromosome segregation, phenotypes commonly associated with impaired histone H3(K9) methylation. Therefore, the key constitutive heterochromatin determinants can dynamically redistribute depending on physiological context but still maintain the essential function(s) of chromosomes. Thus, our data show that cathepsin L stabilizes epigenetic heterochromatin markers on pericentromeric heterochromatin and the Y chromosome through a novel mechanism that does not involve DNA methylation or affect heterochromatin structure and operates on both somatic and sex chromosomes

On the interaction of Mg with the (111) and (110) surfaces of ceria

The catalytic activity of cerium dioxide can be modified by deposition of alkaline earth oxide layers or nanoparticles or by substitutional doping of metal cations at the Ce site in ceria. In order to understand the effect of Mg oxide deposition and doping, a combination of experiment and first principles simulations is a powerful tool. In this paper, we examine the interaction of Mg with the ceria (111) surface using both angle resolved X-ray (ARXPS) and resonant (RPES) photoelectron spectroscopy measurements and density functional theory (DFT) corrected for on-site Coulomb interactions (DFT + U). With DFT + U, we also examine the interaction of Mg with the ceria (110) surface. The experiments show that upon deposition of Mg, Ce ions are reduced to Ce3+, while Mg is oxidised. When Mg is incorporated into ceria, no reduced Ce3+ ions are found and oxygen vacancies are present. The DFT + U simulations show that each Mg that is introduced leads to formation of two reduced Ce3+ ions. When Mg is incorporated at a Ce site in the (111) surface, one oxygen vacancy is formed for each Mg to compensate the different valencies, so that all Ce ions are oxidised. The behaviour of Mg upon interaction with the (110) surface is the same as with the (111) surface. The combined results provide a basis for deeper insights into the catalytic behaviour of ceria-based mixed oxide catalysts

Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus▿

The genomes of positive-strand RNA viruses undergo conformational shifts that complicate efforts to equate structures with function. We have initiated a detailed analysis of secondary and tertiary elements within the 3′ end of Turnip crinkle virus (TCV) that are required for viral accumulation in vivo. MPGAfold, a massively parallel genetic algorithm, suggested the presence of five hairpins (H4a, H4b, and previously identified hairpins H4, H5, and Pr) and one H-type pseudoknot (Ψ3) within the 3′-terminal 194 nucleotides (nt). In vivo compensatory mutagenesis analyses confirmed the existence of H4a, H4b, Ψ3 and a second pseudoknot (Ψ2) previously identified in a TCV satellite RNA. In-line structure probing of the 194-nt fragment supported the coexistence of H4, H4a, H4b, Ψ3 and a pseudoknot that connects H5 and the 3′ end (Ψ1). Stepwise replacements of TCV elements with the comparable elements from Cardamine chlorotic fleck virus indicated that the complete 142-nt 3′ end, and subsets containing Ψ3, H4a, and H4b or Ψ3, H4a, H4b, H5, and Ψ2, form functional domains for virus accumulation in vivo. A new 3-D molecular modeling protocol (RNA2D3D) predicted that H4a, H4b, H5, Ψ3, and Ψ2 are capable of simultaneous existence and bears some resemblance to a tRNA. The related Japanese iris necrotic ring virus does not have comparable domains. These results provide a framework for determining how interconnected elements participate in processes that require 3′ untranslated region sequences such as translation and replication

Surface sites on Pt–CeO2 mixed oxide catalysts probed by CO adsorption: a synchrotron radiation photoelectron spectroscopy study

By means of synchrotron radiation photoemission spectroscopy, we have investigated Pt–CeO2 mixed oxide films prepared on CeO2(111)/Cu(111). Using CO molecules as a probe, we associate the corresponding surface species with specific surface sites. This allows us to identify the changes in the composition and morphology of Pt–CeO2 mixed oxide films caused by annealing in an ultrahigh vacuum. Specifically, two peaks in C 1s spectra at 289.4 and 291.2 eV, associated with tridentate and bidentate carbonate species, are formed on the nanostructured stoichiometric CeO2 film. The peak at 290.5–291.0 eV in the C 1s spectra indicates the onset of restructuring, i.e. coarsening, of the Pt–CeO2 film. This peak is associated with a carbonate species formed near an oxygen vacancy. The onset of cerium oxide reduction is indicated by the peak at 287.8–288.0 eV associated with carbonite species formed near Ce3+ cations. The development of surface species on the Pt–CeO2 mixed oxides suggests that restructuring of the films occurs above 300 K irrespective of Pt loadings. We do not find any adsorbed CO species associated with Pt4+ or Pt2+. The onset of Pt2+ reduction is indicated by the peak at 286.9 eV in the C 1s spectra due to CO adsorption on metallic Pt particles. The thermal stability of Pt2+ in Pt–CeO2 mixed oxide depends on Pt loading. We find excellent stability of Pt2+ for 12% Pt content in the CeO2 film, whereas at a Pt concentration of 25% in the CeO2 film, a large fraction of the Pt2+ is converted into metallic Pt particles above 300 K

Hydrogen activation on Pt–Sn nanoalloys supported on mixed Sn–Ce oxide films

We have studied the interaction of H2 with Pt–Sn nanoalloys supported on Sn–Ce mixed oxide films of different composition by means of synchrotron radiation photoelectron spectroscopy and resonant photoemission spectroscopy. The model catalysts are prepared in a three step procedure that involves (i) the preparation of well-ordered CeO2(111) films on Cu(111) followed by subsequent physical vapor deposition of (ii) metallic Sn and (iii) metallic Pt. The formation of mixed Sn–Ce oxide is accompanied by partial reduction of Ce4+ cations to Ce3+. Pt deposition leads to the formation of Pt–Sn nanoalloys accompanied by the partial re-oxidation of Ce3+ to Ce4+. Subsequent annealing promotes further Pt–Sn alloy formation at expense of the Sn content in the Sn–Ce mixed oxide. Adsorption of H2 on Pt–Sn/Sn–Ce–O at 150 K followed by stepwise annealing results in reversible reduction of Ce cations caused by spillover of dissociated hydrogen between 150 and 300 K. Above 500 K, annealing of Pt–Sn/Sn–Ce–O in a hydrogen atmosphere results in irreversible reduction of Ce cations. This reduction is caused by the reaction of hydrogen with oxygen provided by the mixed oxide substrate via the reverse spillover to Pt–Sn nanoalloy. The extent of the hydrogen and oxygen spillover strongly depends on the amount of Sn in the Sn–Ce mixed-oxide. We observe an enhancement of hydrogen spillover on Pt–Sn/Sn–Ce–O at low Sn concentration as compared to Sn-free Pt/CeO2. Although the extent of hydrogen spillover on Pt–Sn/Sn–Ce–O with high Sn concentration is comparable to Pt/CeO2, the reverse oxygen spillover is substantially suppressed on these samples

The 3′ proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits

During cap-dependent translation of eukaryotic mRNAs, initiation factors interact with the 5′ cap to attract ribosomes. When animal viruses translate in a cap-independent fashion, ribosomes assemble upstream of initiation codons at internal ribosome entry sites (IRES). In contrast, many plant viral genomes do not contain 5′ ends with substantial IRES activity but instead have 3′ translational enhancers that function by an unknown mechanism. A 393-nucleotide (nt) region that includes the entire 3′ UTR of the Turnip crinkle virus (TCV) synergistically enhances translation of a reporter gene when associated with the TCV 5′ UTR. The major enhancer activity was mapped to an internal region of ∼140 nt that partially overlaps with a 100-nt structural domain previously predicted to adopt a form with some resemblance to a tRNA, according to a recent study by J.C. McCormack and colleagues. The T-shaped structure binds to 80S ribosomes and 60S ribosomal subunits, and binding is more efficient in the absence of surrounding sequences and in the presence of a pseudoknot that mimics the tRNA-acceptor stem. Untranslated TCV satellite RNA satC, which contains the TCV 3′ end and 6-nt differences in the region corresponding to the T-shaped element, does not detectably bind to 80S ribosomes and is not predicted to form a comparable structure. Binding of the TCV T-shaped element by 80S ribosomes was unaffected by salt-washing, reduced in the presence of AcPhe-tRNA, which binds to the P-site, and enhanced binding of Phe-tRNA to the ribosome A site. Mutations that reduced translation in vivo had similar effects on ribosome binding in vitro. This strong correlation suggests that ribosome entry in the 3′ UTR is a key function of the 3′ translational enhancer of TCV and that the T-shaped element contains some tRNA-like properties