Atmospheric molecular blobs shape up circumstellar envelopes of AGB stars.

During their thermally pulsing phase, asymptotic giant branch (AGB) stars eject material that forms extended dusty envelopes1. Visible polarimetric imaging found clumpy dust clouds within two stellar radii of several oxygen-rich stars2-6. Inhomogeneous molecular gas has also been observed in multiple emission lines within several stellar radii of different oxygen-rich stars, including W Hya and Mira7-10. At the stellar surface level, infrared images have shown intricate structures around the carbon semiregular variable R Scl and in the S-type star π1 Gru11,12. Infrared images have also shown clumpy dust structures within a few stellar radii of the prototypical carbon AGB star IRC+10°216 (refs. 13,14), and studies of molecular gas distribution beyond the dust formation zone have also shown complex circumstellar structures15. Because of the lack of sufficient spatial resolution, however, the distribution of molecular gas in the stellar atmosphere and the dust formation zone of AGB carbon stars is not known, nor is how it is subsequently expelled. Here we report observations with a resolution of one stellar radius of the recently formed dust and molecular gas in the atmosphere of IRC+10°216. Lines of HCN, SiS and SiC2 appear at different radii and in different clumps, which we interpret as large convective cells in the photosphere, as seen in Betelgeuse16. The convective cells coalesce with pulsation, causing anisotropies that, together with companions17,18, shape its circumstellar envelope.

Oxygen intercalation in PVD graphene grown on copper substrates: A decoupling approach.

We investigate the intercalation process of oxygen in-between a PVD-grown graphene layer and different copper substrates as a methodology for reducing the substrate-layer interaction. This growth method leads to an extended defect-free graphene layer that strongly couples with the substrate. We have found, by means of X-ray photoelectron spectroscopy, that after oxygen exposure at different temperatures, ranging from 280 °C to 550 °C, oxygen intercalates at the interface of graphene grown on Cu foil at an optimal temperature of 500 °C. The low energy electron diffraction technique confirms the adsorption of an atomic oxygen adlayer on top of the Cu surface and below graphene after oxygen exposure at elevated temperature, but no oxidation of the substrate is induced. The emergence of the 2D Raman peak, quenched by the large interaction with the substrate, reveals that the intercalation process induces a structural undoing. As suggested by atomic force microscopy, the oxygen intercalation does not change significantly the surface morphology. Moreover, theoretical simulations provide further insights into the electronic and structural undoing process. This protocol opens the door to an efficient methodology to weaken the graphene-substrate interaction for a more efficient transfer to arbitrary surfaces.

Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy.

Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.

Spectroscopic characterization of the on-surface induced (cyclo)dehydrogenation of a N-heteroaromatic compound on noble metal surfaces.

New nanoarchitectures can be built from polycyclic aromatic hydrocarbons (PAHs) by exploiting the capability of some metal surfaces for inducing cyclodehydrogenation reactions. This bottom-up approach allows the formation of nanostructures with a different dimensionality from the same precursor as a consequence of the diffusion and coupling of the PAHs adsorbed on the surface. In this work we present a thorough study, by means of a combination of X-ray photoemission spectroscopy, near-edge X-ray absorption fine structure and scanning tunneling microscopy with first principle calculations of the structural and chemical transformations undergone by pyridyl-substituted dibenzo[5]helicene on three coinage surfaces, namely Cu(110), Cu(111) and Au(111). Upon annealing, on-surface chemical reactions are promoted affecting the adsorbate/substrate and the molecule/molecule interactions. This thermally induced process favours the transformation from diffusing isolated molecules to polymeric nanographene chains and finally to N-doped graphene.

High-quality PVD graphene growth by fullerene decomposition on Cu foils.

We present a new protocol to grow large-area, high-quality single-layer graphene on Cu foils at relatively low temperatures. We use C60 molecules evaporated in ultra high vacuum conditions as carbon source. This clean environment results in a strong reduction of oxygen-containing groups as depicted by X-ray photoelectron spectroscopy (XPS). Unzipping of C60 is thermally promoted by annealing the substrate at 800ºC during evaporation. The graphene layer extends over areas larger than the Cu crystallite size, although it is changing its orientation with respect to the surface in the wrinkles and grain boundaries, producing a modulated ring in the low energy electron diffraction (LEED) pattern. This protocol is a self-limiting process leading exclusively to one single graphene layer. Raman spectroscopy confirms the high quality of the grown graphene. This layer exhibits an unperturbed Dirac-cone with a clear n-doping of 0.77 eV, which is caused by the interaction between graphene and substrate. Density functional theory (DFT) calculations show that this interaction can be induced by a coupling between graphene and substrate at specific points of the structure leading to a local sp3 configuration, which also contribute to the D-band in the Raman spectra.

Mesophyll conductance to CO2 and Rubisco as targets for improving intrinsic water use efficiency in C3 plants.

Water limitation is a major global constraint for plant productivity that is likely to be exacerbated by climate change. Hence, improving plant water use efficiency (WUE) has become a major goal for the near future. At the leaf level, WUE is the ratio between photosynthesis and transpiration. Maintaining high photosynthesis under water stress, while improving WUE requires either increasing mesophyll conductance (gm ) and/or improving the biochemical capacity for CO2 assimilation-in which Rubisco properties play a key role, especially in C3 plants at current atmospheric CO2 . The goals of the present analysis are: (1) to summarize the evidence that improving gm and/or Rubisco can result in increased WUE; (2) to review the degree of success of early attempts to genetically manipulate gm or Rubisco; (3) to analyse how gm , gsw and the Rubisco's maximum velocity (Vcmax ) co-vary across different plant species in well-watered and drought-stressed conditions; (4) to examine how these variations cause differences in WUE and what is the overall extent of variation in individual determinants of WUE; and finally, (5) to use simulation analysis to provide a theoretical framework for the possible control of WUE by gm and Rubisco catalytic constants vis-à-vis gsw under water limitations.

Diffusional limitations explain the lower photosynthetic capacity of ferns as compared with angiosperms in a common garden study.

Ferns are thought to have lower photosynthetic rates than angiosperms and they lack fine stomatal regulation. However, no study has directly compared photosynthesis in plants of both groups grown under optimal conditions in a common environment. We present a common garden comparison of seven angiosperms and seven ferns paired by habitat preference, with the aims of (1) confirming that ferns do have lower photosynthesis capacity than angiosperms and quantifying these differences; (2) determining the importance of diffusional versus biochemical limitations; and (3) analysing the potential implication of leaf anatomical traits in setting the photosynthesis capacity in both groups. On average, the photosynthetic rate of ferns was about half that of angiosperms, and they exhibited lower stomatal and mesophyll conductance to CO2 (gm ), maximum velocity of carboxylation and electron transport rate. A quantitative limitation analysis revealed that stomatal and mesophyll conductances were co-responsible for the lower photosynthesis of ferns as compared with angiosperms. However, gm alone was the most constraining factor for photosynthesis in ferns. Consistently, leaf anatomy showed important differences between angiosperms and ferns, especially in cell wall thickness and the surface of chloroplasts exposed to intercellular air spaces.

Ortho and para hydrogen dimers on G/SiC(0001): combined STM and DFT study.

The hydrogen (H) dimer structures formed upon room-temperature H adsorption on single layer graphene (SLG) grown on SiC(0001) are addressed using a combined theoretical-experimental approach. Our study includes density functional theory (DFT) calculations for the full (6√3 × 6√3)R30° unit cell of the SLG/SiC(0001) substrate and atomically resolved scanning tunneling microscopy images determining simultaneously the graphene lattice and the internal structure of the H adsorbates. We show that H atoms normally group in chemisorbed coupled structures of different sizes and orientations. We make an atomic scale determination of the most stable experimental geometries, the small dimers and ellipsoid-shaped features, and we assign them to hydrogen adsorbed in para dimers and ortho dimers configuration, respectively, through comparison with the theory.

Adsorption and Coupling of 4-aminophenol on Pt(111) surfaces.

We have deposited 4-aminophenol on Pt(111) surfaces in ultra-high vacuum and studied the strength of its adsorption through a combination of STM, LEED, XPS and ab initio calculations. Although an ordered (2√3×2√3)R30° phase appears, we have observed that molecule-substrate interaction dominates the adsorption geometry and properties of the system. At RT the high catalytic activity of Pt induces aminophenol to lose the H atom from the hydroxyl group, and a proportion of the molecules lose the complete hydroxyl group. After annealing above 420K, all deposited aminophenol molecules have lost the OH moiety and some hydrogen atoms from the amino groups. At this temperature, short single-molecule oligomer chains can be observed. These chains are the product of a new reaction that proceeds via the coupling of radical species that is favoured by surface diffusion.

Assessment of seabed litter at Concepción Seamount (Canary island) using a remotely operated towed vehicle.

The seafloor is recognised as a major sink for marine litter. However, studies conducted in this compartment addressing marine litter densities and its interactions with fauna are scarce, mainly due to sampling constraints. In this paper, we assess marine litter density, composition and interactions with marine communities and evaluate its relationship with fishing activities at the "Banco de la Concepción" seamount (Canary Islands, Spain). We took advantage of underwater video records taken with a Remotely Operated Towed Vehicle in the framework of the LIFE IP INTEMARES project. A total of 56 video transects were analysed covering about 9 km with 19 h of video recording. Transects were categorised as high, low, and null fishing effort based on the Vessel Monitoring System (VMS) positional data registered between 2009 and 2017. Litter items were recorded in 70% of the transects with a mean density of 2122 (±2464) items km-2. There were significant differences in litter densities over the three levels of fishing pressure, with a density decrease from stations of high to stations of null fishing pressure. Regarding categories, plastic was by far the most abundant category found (83.1%), mainly consisting of fishing lines, both monofilaments and entangled longlines. The study of the interactions of marine litter with fauna showed that less than 20% of the items presented an interaction with benthic organisms either by causing or not a visible impact. The sponge Asconema setubalense accounted for more than half (57.4%) of all interactions, but only 5% of all A. setubalense specimens showed physical damage.

n-Alkanes formed by methyl-methylene addition as a source of meteoritic aliphatics.

Aliphatics prevail in asteroids, comets, meteorites and other bodies in our solar system. They are also found in the interstellar and circumstellar media both in gas-phase and in dust grains. Among aliphatics, linear alkanes (n-CnH2n+2) are known to survive in carbonaceous chondrites in hundreds to thousands of parts per billion, encompassing sequences from CH4 to n-C31H64. Despite being systematically detected, the mechanism responsible for their formation in meteorites has yet to be identified. Based on advanced laboratory astrochemistry simulations, we propose a gas-phase synthesis mechanism for n-alkanes starting from carbon and hydrogen under conditions of temperature and pressure that mimic those found in carbon-rich circumstellar envelopes. We characterize the analogs generated in a customized sputter gas aggregation source using a combination of atomically precise scanning tunneling microscopy, non-contact atomic force microscopy and ex-situ gas chromatography-mass spectrometry. Within the formed carbon nanostructures, we identify the presence of n-alkanes with sizes ranging from n-C8H18 to n-C32H66. Ab-initio calculations of formation free energies, kinetic barriers, and kinetic chemical network modelling lead us to propose a gas-phase growth mechanism for the formation of large n-alkanes based on methyl-methylene addition (MMA). In this process, methylene serves as both a reagent and a catalyst for carbon chain growth. Our study provides evidence of an aliphatic gas-phase synthesis mechanism around evolved stars and provides a potential explanation for its presence in interstellar dust and meteorites.

BRCA1 mRNA expression and outcome to neoadjuvant cisplatin-based chemotherapy in bladder cancer.

BACKGROUND: neoadjuvant chemotherapy has shown a modest benefit in muscle-invasive bladder cancer patients; however, the subset of patients most likely to benefit has not been identified. BRCA1 plays a central role in DNA repair pathways and low BRCA1 expression has been associated with sensitivity to cisplatin and longer survival in lung and ovarian cancer patients. PATIENTS AND METHODS: we assessed BRCA1 messenger RNA expression levels in paraffin-embedded pre-treatment tumor samples obtained by transurethral resection from 57 patients with locally advanced bladder cancer subsequently treated with neoadjuvant cisplatin-based chemotherapy. BRCA1 levels were divided into terciles and correlated with pathological response and survival. RESULTS: a significant pathological response (pT0-1) was attained in 66% (24 of 39) of patients with low/intermediate BRCA1 levels compared with 22% (4 of 18) of patients with high BRCA1 levels (P = 0.01). Median survival was 168 months in patients with low/intermediate levels and 34 months in patients with high BRCA1 levels (P = 0.002). In the multivariate analysis for survival, only BRCA1 expression levels and lymphovascular invasion emerged as independent prognostic factors. CONCLUSIONS: our data suggest that BRCA1 expression may predict the efficacy of cisplatin-based neoadjuvant chemotherapy and may help to customize therapy in bladder cancer patients.

Twitter data analysis to assess the interest of citizens on the impact of marine plastic pollution.

Few studies have mined social media platforms to assess environmental concerns. In this study, Twitter was scraped to obtain a ~140,000 tweet dataset related specifically to marine plastic pollution. The goal is to understand what kind of users profiles are tweeting and how and when they do it. In addition, topic modelling and graph theory techniques have allowed us to identify main concerns on this topic: i) impact on wildlife, ii) microplastics/water pollution, iii) estimates/reports, iv) legislation/protection, and v) recycling/cleaning initiatives. Results reveal a scarce influence of organizations involved in research and marine environmental awareness, so some guidelines are depicted that could help to adjust their communication plans. This is relevant to engage society through reliable information, change habits and reinforce sustainable behaviour. A visualization tool has been created to analyze the results over time.

Ectopic expression of the atypical HLH FaPRE1 gene determines changes in cell size and morphology.

PACLOBUTRAZOL RESISTANCE (PRE) genes code atypical HLH transcriptional regulators characterized by the absence of a DNA-binding domain but present an HLH dimerization domain. In vegetative tissues, the function of these HLH proteins has been related with cell elongation processes. In strawberry, three FaPRE genes are expressed, two of them (FaPRE2 and FaPRE3) in vegetative tissues while FaPRE1 is fruit receptacle-specific. Ubiquitous FaPRE1 accumulation produced elongated flower receptacles and plants due to the elongation of the main aerial vegetative organs, with the exception of leaves. Histological analysis clearly demonstrated that the observed phenotype was due to significant changes in the parenchymal cell's morphology. In addition, transcriptomic studies of the transgenic elongated flower receptacles allowed to identify a small group of differentially expressed genes that encode cell wall-modifying enzymes. Together, the data seem to indicate that, in the strawberry plant vegetative organs, FaPRE proteins could modulate the expression of genes related with the determination of the size and shape of the parenchymal cells.

Ordered vacancy network induced by the growth of epitaxial graphene on Pt(111).

We have studied large areas of (√3×√3)R30° graphene commensurate with a Pt(111) substrate. A combination of experimental techniques with ab initio density functional theory indicates that this structure is related to a reconstruction at the Pt surface, consisting of an ordered vacancy network formed in the outermost Pt layer and a graphene layer covalently bound to the Pt substrate. The formation of this reconstruction is enhanced if low temperatures and polycyclic aromatic hydrocarbons are used as molecular precursors for epitaxial growth of the graphene layers.

Interplay between fast diffusion and molecular interaction in the formation of self-assembled nanostructures of S-cysteine on Au(111).

We have studied the first stages leading to the formation of self-assembled monolayers of S-cysteine molecules adsorbed on a Au(111) surface. Density functional theory (DFT) calculations for the adsorption of individual cysteine molecules on Au(111) at room temperature show low-energy barriers all over the 2D Au(111) unit cell. As a consequence, cysteine molecules diffuse freely on the Au(111) surface and they can be regarded as a 2D molecular gas. The balance between molecule-molecule and molecule-substrate interactions induces molecular condensation and evaporation from the morphological surface structures (steps, reconstruction edges, etc.) as revealed by scanning tunnelling microscopy (STM) images. These processes lead progressively to the formation of a number of stable arrangements, not previously reported, such as single-molecular rows, trimers, and 2D islands. The condensation of these structures is driven by the aggregation of new molecules, stabilized by the formation of electrostatic interactions between adjacent NH(3)(+) and COO(-) groups, together with adsorption at a slightly more favorable quasi-top site of the herringbone Au reconstruction.

Understanding atomic-resolved STM images on TiO2(110)-(1 x 1) surface by DFT calculations.

We present a combination of experimental STM images and DFT calculations to understand the atomic scale contrast of features found in high-resolution STM images. Simulating different plausible structural models for the tip, we have been able to reproduce various characteristics previously reported in experimental images on TiO(2)(110)-(1 x 1) under controlled UHV conditions. Our results allow us to determine the influence of different chemical and morphological tip terminations on the atomic-resolution STM images of the TiO(2)(110)-(1 x 1) surface. The commonest images have been properly explained using standard models for a W tip, either clean or with a single O atom located at the apex. Furthermore, a double transfer of oxygen atoms can account for different types of bizarre atomic-resolution features occasionally seen, and not conclusively interpreted before. Importantly, we discuss how typical point-defects are imaged on this surface by different tips, namely bridging O vacancies and adsorbed OH groups.

Chemical equilibrium in AGB atmospheres: Successes, failures, and prospects for small molecules, clusters, and condensates.

Chemical equilibrium has proven extremely useful for predicting the chemical composition of AGB atmospheres. Here we use a recently developed code and an updated thermochemical database that includes gaseous and condensed species involving 34 elements to compute the chemical equilibrium composition of AGB atmospheres of M-, S-, and C-type stars. We include for the first time Ti x C y clusters, with x = 1-4 and y = 1-4, and selected larger clusters ranging up to Ti13C22, for which thermochemical data are obtained from quantum-chemical calculations. Our main aims are to systematically survey the main reservoirs of each element in AGB atmospheres, review the successes and failures of chemical equilibrium by comparing it with the latest observational data, identify potentially detectable molecules that have not yet been observed, and diagnose the most likely gas-phase precursors of dust and determine which clusters might act as building blocks of dust grains. We find that in general, chemical equilibrium reproduces the observed abundances of parent molecules in circumstellar envelopes of AGB stars well. There are, however, severe discrepancies of several orders of magnitude for some parent molecules that are observed to be anomalously overabundant with respect to the predictions of chemical equilibrium. These are HCN, CS, NH3, and SO2 in M-type stars, H2O and NH3 in S-type stars, and the hydrides H2O, NH3, SiH4, and PH3 in C-type stars. Several molecules have not yet been observed in AGB atmospheres but are predicted with non-negligible abundances and are good candidates for detection with observatories such as ALMA. The most interesting ones are SiC5, SiNH, SiCl, PS, HBO, and the metal-containing molecules MgS, CaS, CaOH, CaCl, CaF, ScO, ZrO, VO, FeS, CoH, and NiS. In agreement with previous studies, the first condensates predicted to appear in C-rich atmospheres are found to be carbon, TiC, and SiC, while Al2O3 is the first major condensate expected in O-rich outflows. According to our chemical equilibrium calculations, the gas-phase precursors of carbon dust are probably acetylene, atomic carbon, and/or C3, while for silicon carbide dust, the most likely precursors are the molecules SiC2 and Si2C. In the case of titanium carbide dust, atomic Ti is the major reservoir of this element in the inner regions of AGB atmospheres, and therefore it is probably the main supplier of titanium during the formation of TiC dust. However, chemical equilibrium predicts that large titanium-carbon clusters such as Ti8C12 and Ti13C22 become the major reservoirs of titanium at the expense of atomic Ti in the region where condensation of TiC is expected to occur. This suggests that the assembly of large Ti x C y clusters might be related to the formation of the first condensation nuclei of TiC. In the case of Al2O3 dust, chemical equilibrium indicates that atomic Al and the carriers of Al-O bonds AlOH, AlO, and Al2O are the most likely gas-phase precursors.

Production of nanohole/nanodot patterns on Si(001) by ion beam sputtering with simultaneous metal incorporation.

We have established the conditions for which nanohole and nanodot patterns are produced on Si(001) surfaces by 1 keV Ar(+) ion beam sputtering (IBS) at normal incidence with an alternating cold cathode ion source (ACC-IS). Nanohole patterns are produced within a narrow IBS window for low ion fluxes (<100 µA cm(-2)) and relatively low ion fluences (<10(18) ions cm(-2)) whereas nanodot morphologies are produced above this window. The nanohole pattern is not stable after prolonged irradiation since it evolves to a nanodot morphology. Rutherford backscattering spectrometry (RBS) measurements show that nanohole patterns are produced when the metal content on the irradiated surfaces is higher (within (2.5-3.5 × 10(15)) atoms cm(-2)) than in the case of nanodots (<2.5 × 10(15) atoms cm(-2)). The different metal content is related to the ACC-IS operation, since the set-up provides simultaneous incorporation of Fe and Mo on the target surface from the erosion of the cathodes and sample holder, respectively. The role of metal incorporation on pattern selectivity has been corroborated qualitatively by extending the results obtained with the ACC-IS to a standard Kaufman-type source. In order to gain further information on the metal effects, chemical analysis of the surface has been performed to complement the compositional RBS results, showing for the first time the relevant participation of metal silicides. Further outlook and a discussion regarding the role of metal incorporation are also given.

Reversible Graphene decoupling by NaCl photo-dissociation.

We describe the reversible intercalation of Na under graphene on Ir(111) by photo-dissociation of a previously adsorbed NaCl overlayer. After room temperature evaporation, NaCl adsorbs on top of graphene forming a bilayer. With a combination of electron diffraction and photoemission techniques we demonstrate that the NaCl overlayer dissociates upon a short exposure to an X-ray beam. As a result, chlorine desorbs while sodium intercalates under the graphene, inducing an electronic decoupling from the underlying metal. Low energy electron diffraction shows the disappearance of the moiré pattern when Na intercalates between graphene and iridium. Analysis of the Na 2p core-level by X-ray photoelectron spectroscopy shows a chemical change from NaCl to metallic buried Na at the graphene/Ir interface. The intercalation-decoupling process leads to a n-doped graphene due to the charge transfer from the Na, as revealed by constant energy angle resolved X-ray photoemission maps. Moreover, the process is reversible by a mild annealing of the samples without damaging the graphene.