Reconstructing an ancient fish: Three-dimensional skeletal restoration of the head of Mawsonia (Sarcopterygii, Actinistia) using CT scan, and an adjusted model for body size estimation in fossil coelacanths.

Mawsonia constitutes one of the most conspicuous fossil coelacanth taxa, due to its unique anatomy and possible maximum body size. It typifies Mesozoic coelacanth morphology, before the putative disappearance of the group in the fossil record. In this work, the three-dimensional cranial anatomy and body size estimations of this genus are re-evaluated from a recently described specimen from Upper Jurassic deposits of Uruguay. The 3D restoration was performed directly on the material based on anatomical information provided by the living coelacanth Latimeria and previous two-dimensional restorations of the head of Mawsonia. The montage was then scanned with computed tomography and virtually adjusted to generate an interactive online resource for future anatomical, taxonomic and biomechanical research. In general terms, the model constitutes a tool to improve both the anatomical knowledge of this genus and its comparison with other coelacanths. It also facilitates the evaluation of possible evolutionary trends and the discussion of particular features with potential palaeobiological implications, such as the anterior position of the eye and the development of the pseudomaxillary fold. Regarding the body size, a previous model for body size estimation based on the gular plate was submitted to OLS, RMA, segmented linear and PGLS regressions (including the evaluation of regression statistics, variance analysis, t-tests and residual analysis). The results point to a power relationship between gular and total lengths showing a better support than a simple linear relationship. The new resulting equations were applied to the studied individual and are provided for future estimates. Although an isometric evolutionary growth cannot be rejected with the available evidence, additional models developed with other bones will be necessary to evaluate possible hidden evolutionary allometric trends in this group of fishes, thus avoiding overestimates.

Silicon-Lattice-Matched Boron-Doped Gallium Phosphide: A Scalable Acousto-Optic Platform.

The compact size, scalability, and strongly confined fields in integrated photonic devices enable new functionalities in photonic networking and information processing, both classical and quantum. Gallium phosphide (GaP) is a promising material for active integrated photonics due to its high refractive index, wide bandgap, strong nonlinear properties, and large acousto-optic figure of merit. This study demonstrates that silicon-lattice-matched boron-doped GaP (BGaP), grown at the 12-inch wafer scale, provides similar functionalities as GaP. BGaP optical resonators exhibit intrinsic quality factors exceeding 25,000 and 200,000 at visible and telecom wavelengths, respectively. It further demonstrates the electromechanical generation of low-loss acoustic waves and an integrated acousto-optic (AO) modulator. High-resolution spatial and compositional mapping, combined with ab initio calculations, indicate two candidates for the excess optical loss in the visible band: the silicon-GaP interface and boron dimers. These results demonstrate the promise of the BGaP material platform for the development of scalable AO technologies at telecom and provide potential pathways toward higher performance at shorter wavelengths.

Nanoscale characterization of the sequestration and transformation of silver and arsenic in soil organic matter using atom probe tomography and transmission electron microscopy.

This study investigates the sequestration and transformation of silver (Ag) and arsenic (As) ions in soil organic matter (OM) at the nanoscale using the combination of atom probe tomography (APT), transmission electron microscopy (TEM), focused ion beam (FIB), ion mill thinning and scanning electron microscopy (SEM). Silver-arsenic contaminated organic-rich soils were collected along the shore of Cobalt Lake, a former mining and milling site of the famous Ag deposits at Cobalt, Ontario, Canada. SEM examinations show that particulate organic matter (OM grains) contains mineral inclusions composed of mainly Fe, S, and Si with minor As and traces of Ag. Four OM grains with detectable concentrations of Ag (by SEM-EDS) were further characterized with either a combination of TEM and APT or TEM alone. These examinations show that As is predominantly sequestered by OM through either co-precipitation with Fe-(hydr)oxide inclusions or adsorption on Fe-(hydr)oxides and their subsequent transformation into scorodite (FeAsO4·2H2O)/amorphous Fe-arsenate (AFA). Silver nanoparticles (NPs) with diameters in the range of ∼5-20 nm occur in the organic matrix as well as on the surface of Fe-rich inclusions (Fe-hydroxides, Fe-arsenates, Fe-sulfides), whereas Ag sulfide NPs were only observed on the surfaces of the Fe-rich inclusions. Rims of Ag-sulfides on Ag NPs (TEM data), accumulation of S atoms within and around Ag NPs (APT data), and the occurrence of dendritic as well as euhedral acanthite NPs with diameters in the range of ∼100-400 nm (TEM data) indicate that the sulfidation of the Ag NPs occurred via a mineral-replacement reaction (rims) or a complete dissolution of the Ag NPs, the subsequent precipitation of acanthite NPs and their aggregation (dendrites) and Ostwald ripening (euhedral crystals). These results show the importance of OM and, specifically the mineral inclusions in the sequestration of Ag and As to less bioavailable forms such as acanthite and scorodite, respectively.

Atom probe tomography and transmission electron microscopy: a powerful combination to characterize the speciation and distribution of Cu in organic matter.

The large surface areas in porous organic matter (OM) and on the surface of altered minerals control the sequestration of metal(loid)s in contaminated soils and sediments. This study explores the sequestration of Cu by OM in surficial forest soil in close proximity to the Horne smelter, Rouyn-Noranda, Quebec, Canada. The organic-rich soils have elevated concentrations of Cu (Cu = 〈0.75〉 wt%) but lack associations between organic matter (OM) and Cu-sulfides, commonly observed in organic-rich Cu-contaminated soils. This provides a unique opportunity to study the sequestration of Cu by OM in a sulfur-depleted environment using a combination of scanning electron microscopy (SEM), transmission electron microscopy (TEM) and atom probe tomography (APT). In two examined OM particles, Cu is predominantly sequestered as (I) nano- to micrometer-size Cu-bearing spinels, (II) as cuprite (Cu2O) nanoparticles or (III) finely dispersed Cu in association with clusters of magnetite (Fe3O4) nanoparticles embedded in amorphous silica-rich pockets and (IV) in the OM matrix. The occurrence of euhedral crystals and nanoparticles in the single-digit range within the OM matrix indicate that the majority of the nanoparticles formed in situ within the OM particles. A model is developed which proposes that the sequestration of Cu in OM is promoted by (I) the partial mineralization of the OM matrix by amorphous silica; (II) the nucleation of magnetite nanoparticles on highly reactive silanol groups; (III) the diffusion of Cu within mineralized and altered areas of the OM; (IV) the availability of Cu-bearing species, which in turn is controlled by the hydrodynamic properties of the pore channels; (V) the formation of precursors and nucleation of Cu-bearing nanoparticles. This study shows that the combination of SEM, TEM and APT provides new insights into the sequestration of metal contaminants by OM at various scales ranging from the single-digit nano- to micrometer scale.

Efficient conversion of low-concentration nitrate sources into ammonia on a Ru-dispersed Cu nanowire electrocatalyst.

Electrochemically converting nitrate ions, a widely distributed nitrogen source in industrial wastewater and polluted groundwater, into ammonia represents a sustainable route for both wastewater treatment and ammonia generation. However, it is currently hindered by low catalytic activities, especially under low nitrate concentrations. Here we report a high-performance Ru-dispersed Cu nanowire catalyst that delivers an industrial-relevant nitrate reduction current of 1 A cm-2 while maintaining a high NH3 Faradaic efficiency of 93%. More importantly, this high nitrate-reduction catalytic activity enables over a 99% nitrate conversion into ammonia, from an industrial wastewater level of 2,000 ppm to a drinkable water level <50 ppm, while still maintaining an over 90% Faradaic efficiency. Coupling the nitrate reduction effluent stream with an air stripping process, we successfully obtained high purity solid NH4Cl and liquid NH3 solution products, which suggests a practical approach to convert wastewater nitrate into valuable ammonia products. Density functional theory calculations reveal that the highly dispersed Ru atoms provide active nitrate reduction sites and the surrounding Cu sites can suppress the main side reaction, the hydrogen evolution reaction.

Fungal hyphae develop where titanomagnetite inclusions reach the surface of basalt grains.

Nutrient foraging by fungi weathers rocks by mechanical and biochemical processes. Distinguishing fungal-driven transformation from abiotic mechanisms in soil remains a challenge due to complexities within natural field environments. We examined the role of fungal hyphae in the incipient weathering of granulated basalt from a three-year field experiment in a mixed hardwood-pine forest (S. Carolina) to identify alteration at the nanometer to micron scales based on microscopy-tomography analyses. Investigations of fungal-grain contacts revealed (i) a hypha-biofilm-basaltic glass interface coinciding with titanomagnetite inclusions exposed on the grain surface and embedded in the glass matrix and (ii) native dendritic and subhedral titanomagnetite inclusions in the upper 1-2 µm of the grain surface that spanned the length of the fungal-grain interface. We provide evidence of submicron basaltic glass dissolution occurring at a fungal-grain contact in a soil field setting. An example of how fungal-mediated weathering can be distinguished from abiotic mechanisms in the field was demonstrated by observing hyphal selective occupation and hydrolysis of glass-titanomagnetite surfaces. We hypothesize that the fungi were drawn to basaltic glass-titanomagnetite boundaries given that titanomagnetite exposed on or very near grain surfaces represents a source of iron to microbes. Furthermore, glass is energetically favorable to weathering in the presence of titanomagnetite. Our observations demonstrate that fungi interact with and transform basaltic substrates over a three-year time scale in field environments, which is central to understanding the rates and pathways of biogeochemical reactions related to nuclear waste disposal, geologic carbon storage, nutrient cycling, cultural artifact preservation, and soil-formation processes.

Spontaneous phase segregation of Sr2NiO3 and SrNi2O3 during SrNiO3 heteroepitaxy.

Recent discovery of superconductivity in Nd0.8Sr0.2NiO2 motivates the synthesis of other nickelates for providing insights into the origin of high-temperature superconductivity. However, the synthesis of stoichiometric R 1-x Sr x NiO3 thin films over a range of x has proven challenging. Moreover, little is known about the structures and properties of the end member SrNiO3 Here, we show that spontaneous phase segregation occurs while depositing SrNiO3 thin films on perovskite oxide substrates by molecular beam epitaxy. Two coexisting oxygen-deficient Ruddlesden-Popper phases, Sr2NiO3 and SrNi2O3, are formed to balance the stoichiometry and stabilize the energetically preferred Ni2+ cation. Our study sheds light on an unusual oxide thin-film nucleation process driven by the instability in perovskite structured SrNiO3 and the tendency of transition metal cations to form their most stable valence (i.e., Ni2+ in this case). The resulting metastable reduced Ruddlesden-Popper structures offer a testbed for further studying emerging phenomena in nickel-based oxides.

Calcareous organic matter coatings sequester siderophores in alkaline soils.

Although most studies of organic matter (OM) stabilization in soils have focused on adsorption to aluminosilicate and iron-oxide minerals due to their strong interactions with organic nucleophiles, stabilization within alkaline soils has been empirically correlated with exchangeable Ca. Yet the extent of competing processes within natural soils remains unclear because of inadequate characterization of soil mineralogy and OM distribution within the soil in relation to minerals, particularly in C poor alkaline soils. In this study, we employed bulk and surface-sensitive spectroscopic methods including X-ray diffraction, 57Fe-Mössbauer, and X-ray photoemission spectroscopy (XPS), and transmission electron microscopy (TEM) methods to investigate the minerology and soil organic C and N distribution on individual fine particles within an alkaline soil. Microscopy and XPS analyses demonstrated preferential sorption of Ca-containing OM onto surfaces of Fe-oxides and calcite. This result was unexpected given that the bulk combined amounts of quartz and Fe-containing feldspars of the soil constitute ~90% of total minerals and the surface atomic composition was largely Fe and Al (>10% combined) compared to Ca (4.2%). Soil sorption experiments were conducted with two siderophores, pyoverdine and enterobactin, to evaluate the adsorption of organic molecules with functional groups that strongly and preferentially bind Fe. A greater fraction of pyoverdine was adsorbed compared to enterobactin, which is smaller, less polar, and has a lower aqueous solubility. Using NanoSIMS to map the distribution of isotopically-labeled siderophores, we observed correlations with Ca and Fe, along with strong isotopic dilution with native C, indicating associations with OM coatings rather than with bare mineral surfaces. We propose a mechanism of adsorption by which organics aggregate within alkaline soils via cation bridging, favoring the stabilization of larger molecules with a greater number of nucleophilic functional groups.

Directional Gateway to Metal Oxidation: 3D Chemical Mapping Unfolds Oxygen Diffusional Pathways in Rhodium Nanoparticles.

The interaction of oxygen with a reactive metal is ubiquitous, yet the precise atomic-level mechanisms and pathways leading to the formation of a surface oxide are not well-understood. We report oxygen atom distributions inside Rh single nanoparticles using atom probe microscopy (APM) and demonstrate that mainly facets of the ⟨022̅⟩ crystallographic directions act as oxygen-permeable gateways. The highly anisotropic spatial distribution of incorporated oxygen atoms is in agreement with video-field emission analyses according to which {113} facets of the ⟨022̅⟩ zones act as portals for subsurface diffusion. In addition to providing a more fundamental understanding of the precursor states to metal corrosion, in particular for the case of nanosized metal particles, our studies are also relevant for heterogeneous catalysis where catalytic activity and selectivity conform to reaction-induced structural changes of metal nanoparticles.

Visualizing the iron atom exchange front in the Fe(II)-catalyzed recrystallization of goethite by atom probe tomography.

The autocatalytic redox interaction between aqueous Fe(II) and Fe(III)-(oxyhydr)oxide minerals such as goethite and hematite leads to rapid recrystallization marked, in principle, by an atom exchange (AE) front, according to bulk iron isotopic tracer studies. However, direct evidence for this AE front has been elusive given the analytical challenges of mass-resolved imaging at the nanoscale on individual crystallites. We report successful isolation and characterization of the AE front in goethite microrods by 3D atom probe tomography (APT). The microrods were reacted with Fe(II) enriched in tracer 57Fe at conditions consistent with prior bulk studies. APT analyses and 3D reconstructions on cross-sections of the microrods reveal an AE front that is spatially heterogeneous, at times penetrating several nanometers into the lattice, in a manner consistent with defect-accelerated exchange. Evidence for exchange along microstructural domain boundaries was also found, suggesting another important link between exchange extent and initial defect content. The findings provide an unprecedented view into the spatial and temporal characteristics of Fe(II)-catalyzed recrystallization at the atomic scale, and substantiate speculation regarding the role of defects controlling the dynamics of electron transfer and AE interaction at this important redox interface.

Ret receptor tyrosine kinase sustains proliferation and tissue maturation in intestinal epithelia.

Expression of the Ret receptor tyrosine kinase is a defining feature of enteric neurons. Its importance is underscored by the effects of its mutation in Hirschsprung disease, leading to absence of gut innervation and severe gastrointestinal symptoms. We report a new and physiologically significant site of Ret expression in the intestine: the intestinal epithelium. Experiments in Drosophila indicate that Ret is expressed both by enteric neurons and adult intestinal epithelial progenitors, which require Ret to sustain their proliferation. Mechanistically, Ret is engaged in a positive feedback loop with Wnt/Wingless signalling, modulated by Src and Fak kinases. We find that Ret is also expressed by the developing intestinal epithelium of mice, where its expression is maintained into the adult stage in a subset of enteroendocrine/enterochromaffin cells. Mouse organoid experiments point to an intrinsic role for Ret in promoting epithelial maturation and regulating Wnt signalling. Our findings reveal evolutionary conservation of the positive Ret/Wnt signalling feedback in both developmental and homeostatic contexts. They also suggest an epithelial contribution to Ret loss-of-function disorders such as Hirschsprung disease.

An environmental transfer hub for multimodal atom probe tomography.

Environmental control during transfer between instruments is required for samples sensitive to air or thermal exposure to prevent morphological or chemical changes prior to analysis. Atom probe tomography is a rapidly expanding technique for three-dimensional structural and chemical analysis, but commercial instruments remain limited to loading specimens under ambient conditions. In this study, we describe a multifunctional environmental transfer hub allowing controlled cryogenic or room-temperature transfer of specimens under atmospheric or vacuum pressure conditions between an atom probe and other instruments or reaction chambers. The utility of the environmental transfer hub is demonstrated through the acquisition of previously unavailable mass spectral analysis of an intact organic molecule made possible via controlled cryogenic transfer into the atom probe using the hub. The ability to prepare and transfer specimens in precise environments promises a means to access new science across many disciplines from untainted samples and allow downstream time-resolved in situ atom probe studies.

Nanometer-Scale Chemistry of a Calcite Biomineralization Template: Implications for Skeletal Composition and Nucleation.

Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales. Understanding the role of templates in biomineral nucleation, and their importance in skeletal geochemistry requires an integrated, multiscale approach, which can place atom-scale observations of organic-mineral interfaces within a broader structural and geochemical context. Here we map the chemistry of an embedded organic template structure within a carbonate skeleton of the foraminifera Orbulina universa using both atom probe tomography (APT), a 3D chemical imaging technique with Ångström-level spatial resolution, and time-of-flight secondary ionization mass spectrometry (ToF-SIMS), a 2D chemical imaging technique with submicron resolution. We quantitatively link these observations, revealing that the organic template in O. universa is uniquely enriched in both Na and Mg, and contributes to intraskeletal chemical heterogeneity. Our APT analyses reveal the cation composition of the organic surface, offering evidence to suggest that cations other than Ca2+, previously considered passive spectator ions in biomineral templating, may be important in defining the energetics of carbonate nucleation on organic templates.

Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin.

Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Uranium isotopic ratio measurements of U3O8 reference materials by atom probe tomography.

We report results of measurements of isotopic ratios obtained with atom probe tomography on U3O8 reference materials certified for their isotopic abundances of uranium. The results show good agreement with the certified values. High backgrounds due to tails from adjacent peaks complicate the measurement of the integrated peak areas as well as the fact that only oxides of uranium appear in the spectrum, the most intense of which is doubly charged. In addition, lack of knowledge of other instrumental parameters, such as the dead time, may bias the results. Isotopic ratio measurements can be performed at the nanometer-scale with the expectation of sensible results. The abundance sensitivity and mass resolving power of the mass spectrometer are not sufficient to compete with magnetic-sector instruments but are not far from measurements made by ToF-SIMS of other isotopic systems. The agreement of the major isotope ratios is more than sufficient to distinguish most anthropogenic compositions from natural.

Determining the location and nearest neighbours of aluminium in zeolites with atom probe tomography.

Zeolite catalysis is determined by a combination of pore architecture and Brønsted acidity. As Brønsted acid sites are formed by the substitution of AlO4 for SiO4 tetrahedra, it is of utmost importance to have information on the number as well as the location and neighbouring sites of framework aluminium. Unfortunately, such detailed information has not yet been obtained, mainly due to the lack of suitable characterization methods. Here we report, using the powerful atomic-scale analysis technique known as atom probe tomography, the quantitative spatial distribution of individual aluminium atoms, including their three-dimensional extent of segregation. Using a nearest-neighbour statistical analysis, we precisely determine the short-range distribution of aluminium over the different T-sites and determine the most probable Al-Al neighbouring distance within parent and steamed ZSM-5 crystals, as well as assess the long-range redistribution of aluminium upon zeolite steaming.

The Ret receptor regulates sensory neuron dendrite growth and integrin mediated adhesion.

Neurons develop highly stereotyped receptive fields by coordinated growth of their dendrites. Although cell surface cues play a major role in this process, few dendrite specific signals have been identified to date. We conducted an in vivo RNAi screen in Drosophila class IV dendritic arborization (C4da) neurons and identified the conserved Ret receptor, known to play a role in axon guidance, as an important regulator of dendrite development. The loss of Ret results in severe dendrite defects due to loss of extracellular matrix adhesion, thus impairing growth within a 2D plane. We provide evidence that Ret interacts with integrins to regulate dendrite adhesion via rac1. In addition, Ret is required for dendrite stability and normal F-actin distribution suggesting it has an essential role in dendrite maintenance. We propose novel functions for Ret as a regulator in dendrite patterning and adhesion distinct from its role in axon guidance.

Effects of laser energy and wavelength on the analysis of LiFePO4 using laser assisted atom probe tomography.

The effects of laser wavelength (355 nm and 532 nm) and laser pulse energy on the quantitative analysis of LiFePO4 by atom probe tomography are considered. A systematic investigation of ultraviolet (UV, 355 nm) and green (532 nm) laser assisted field evaporation has revealed distinctly different behaviors. With the use of a UV laser, the major issue was identified as the preferential loss of oxygen (up to 10 at%) while other elements (Li, Fe and P) were observed to be close to nominal ratios. Lowering the laser energy per pulse to 1 pJ/pulse from 50 pJ/pulse increased the observed oxygen concentration to nearer its correct stoichiometry, which was also well correlated with systematically higher concentrations of (16)O2(+) ions. Green laser assisted field evaporation led to the selective loss of Li (~33% deficiency) and a relatively minor O deficiency. The loss of Li is likely a result of selective dc evaporation of Li between or after laser pulses. Comparison of the UV and green laser data suggests that the green wavelength energy was absorbed less efficiently than the UV wavelength because of differences in absorption at 355 and 532 nm for LiFePO4. Plotting of multihit events on Saxey plots also revealed a strong neutral O2 loss from molecular dissociation, but quantification of this loss was insufficient to account for the observed oxygen deficiency.