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.

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.

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.

Bithorax-complex genes sculpt the pattern of leucokinergic neurons in the Drosophila central nervous system.

Although the Hox genes are the main factors involved in the generation of diversity along the anterior/posterior body axis of segmented organisms, it is still largely unknown how these genes act in single cells to determine specific traits at precise developmental stages. The aim of this study was to understand the mechanisms by which Hox genes of the Bithorax complex (Bx-C) of Drosophila act to define segmental differences in the ventral nerve cord of the central nervous system. To achieve this, we have focused on the specification of the leucokinin-expressing neurons. We find that these neurons are specified from the same progenitor neuroblast at two different developmental stages: embryonic and larval neurogenesis. We show that genes of the Bx-C acted in postmitotic cells to specify the segment-specific appearance of leucokinergic cells in the larval and adult ventral nerve cord.

Remote control of renal physiology by the intestinal neuropeptide pigment-dispersing factor in Drosophila.

The role of the central neuropeptide pigment-dispersing factor (PDF) in circadian timekeeping in Drosophila is remarkably similar to that of vasoactive intestinal peptide (VIP) in mammals. Like VIP, PDF is expressed outside the circadian network by neurons innervating the gut, but the function and mode of action of this PDF have not been characterized. Here we investigate the visceral roles of PDF by adapting cellular and physiological methods to the study of visceral responses to PDF signaling in wild-type and mutant genetic backgrounds. We find that intestinal PDF acts at a distance on the renal system, where it regulates ureter contractions. We show that PdfR, PDF's established receptor, is expressed by the muscles of the excretory system, and present evidence that PdfR-induced cAMP increases underlie the myotropic effects of PDF. These findings extend the similarities between PDF and VIP beyond their shared central role as circadian regulators, and uncover an unexpected endocrine mode of myotropic action for an intestinal neuropeptide on the renal system.

Bending-induced symmetry breaking of lithiation in germanium nanowires.

From signal transduction of living cells to oxidation and corrosion of metals, mechanical stress intimately couples with chemical reactions, regulating these biological and physiochemical processes. The coupled effect is particularly evident in the electrochemical lithiation/delithiation cycling of high-capacity electrodes, such as silicon (Si), where on the one hand lithiation-generated stress mediates lithiation kinetics and on the other the electrochemical reaction rate regulates stress generation and mechanical failure of the electrodes. Here we report for the first time the evidence on the controlled lithiation in germanium nanowires (GeNWs) through external bending. Contrary to the symmetric core-shell lithiation in free-standing GeNWs, we show bending the GeNWs breaks the lithiation symmetry, speeding up lithaition at the tensile side while slowing down at the compressive side of the GeNWs. The bending-induced symmetry breaking of lithiation in GeNWs is further corroborated by chemomechanical modeling. In the light of the coupled effect between lithiation kinetics and mechanical stress in the electrochemical cycling, our findings shed light on strain/stress engineering of durable high-rate electrodes and energy harvesting through mechanical motion.

Identification of an intrinsic source of doping inhomogeneity in vapor-liquid-solid-grown nanowires.

The vapor-liquid-solid (VLS) process of semiconductor nanowire growth is an attractive approach to low-dimensional materials and heterostructures because it provides a mechanism to modulate, in situ, nanowire composition and doping, but the ultimate limits on doping control are ultimately dictated by the growth process itself. Under widely used conditions for the chemical vapor deposition growth of Si and Ge nanowires from a Au catalyst droplet, we find that dopants incorporated from the liquid are not uniformly distributed. Specifically, atom probe tomographic analysis revealed up to 100-fold enhancements in dopant concentration near the VLS trijunction in both B-doped Si and P-doped Ge nanowires. We hypothesize that radial and azimuthal inhomogeneities arise from a faceted liquid-solid interface present during nanowire growth, and we present a simple model to account for the distribution. As the same segregation behavior was observed in two distinct semiconductors with different dopants, the observed inhomogeneity is likely to be present in other VLS grown nanowires.

Electron-rich driven electrochemical solid-state amorphization in Li-Si alloys.

The physical and chemical behaviors of materials used in energy storage devices, such as lithium-ion batteries (LIBs), are mainly controlled by an electrochemical process, which normally involves insertion/extraction of ions into/from a host lattice with a concurrent flow of electrons to compensate charge balance. The fundamental physics and chemistry governing the behavior of materials in response to the ions insertion/extraction is not known. Herein, a combination of in situ lithiation experiments and large-scale ab initio molecular dynamics simulations are performed to explore the mechanisms of the electrochemically driven solid-state amorphization in Li-Si systems. We find that local electron-rich condition governs the electrochemically driven solid-state amorphization of Li-Si alloys. This discovery provides the fundamental explanation of why lithium insertion in semiconductor and insulators leads to amorphization, whereas in metals, it leads to a crystalline alloy. The present work correlates electrochemically driven reactions with ion insertion, electron transfer, lattice stability, and phase equilibrium.

Demonstration of an electrochemical liquid cell for operando transmission electron microscopy observation of the lithiation/delithiation behavior of Si nanowire battery anodes.

Over the past few years, in situ transmission electron microscopy (TEM) studies of lithium ion batteries using an open-cell configuration have helped us to gain fundamental insights into the structural and chemical evolution of the electrode materials in real time. In the standard open-cell configuration, the electrolyte is either solid lithium oxide or an ionic liquid, which is point-contacted with the electrode. This cell design is inherently different from a real battery, where liquid electrolyte forms conformal contact with electrode materials. The knowledge learnt from open cells can deviate significantly from the real battery, calling for operando TEM technique with conformal liquid electrolyte contact. In this paper, we developed an operando TEM electrochemical liquid cell to meet this need, providing the configuration of a real battery and in a relevant liquid electrolyte. To demonstrate this novel technique, we studied the lithiation/delithiation behavior of single Si nanowires. Some of lithiation/delithation behaviors of Si obtained using the liquid cell are consistent with the results from the open-cell studies. However, we also discovered new insights different from the open cell configuration-the dynamics of the electrolyte and, potentially, a future quantitative characterization of the solid electrolyte interphase layer formation and structural and chemical evolution.

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.

Axial SiGe heteronanowire tunneling field-effect transistors.

We present silicon-compatible trigated p-Ge/i-Si/n-Si axial heteronanowire tunneling field-effect transistors (TFETs), where on-state tunneling occurs in the Ge drain section, while off-state leakage is dominated by the Si junction in the source. Our TFETs have high I(ON) ~ 2 µA/µm, fully suppressed ambipolarity, and a subthreshold slope SS ~ 140 mV/decade over 4 decades of current with lowest SS ~ 50 mV/decade. Device operation in the tunneling mode is confirmed by three-dimensional TCAD simulation. Interestingly, in addition to the TFET mode, our devices work as standard nanowire FETs with a good I(ON)/I(OFF) ratio when the source-drain junction is forward-biased. The improved transport in both biasing modes confirms the benefits of utilizing bandgap engineered axial nanowires for enhancing device performance.

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.

Controlling heterojunction abruptness in VLS-grown semiconductor nanowires via in situ catalyst alloying.

For advanced device applications, increasing the compositional abruptness of axial heterostructured and modulation doped nanowires is critical for optimizing performance. For nanowires grown from metal catalysts, the transition region width is dictated by the solute solubility within the catalyst. For example, as a result of the relatively high solubility of Si and Ge in liquid Au for vapor-liquid-solid (VLS) grown nanowires, the transition region width between an axial Si-Ge heterojunction is typically on the order of the nanowire diameter. When the solute solubility in the catalyst is lowered, the heterojunction width can be made sharper. Here we show for the first time the systematic increase in interface sharpness between axial Ge-Si heterojunction nanowires grown by the VLS growth method using a Au-Ga alloy catalyst. Through in situ tailoring of the catalyst composition using trimethylgallium, the Ge-Si heterojunction width is systematically controlled by tuning the semiconductor solubility within a metal Au-Ga alloy catalyst. The present approach of alloying to control solute solubilities in the liquid catalyst may be extended to increasing the sharpness of axial dopant profiles, for example, in Si-Ge pn-heterojunction nanowires which is important for such applications as nanowire tunnel field effect transistors or in Si pn-junction nanowires.

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.

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.

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.

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.

Temporal and spatial windows delimit activation of the outer ring of wingless in the Drosophila wing.

Extracellular signalling molecules play many roles in the development of higher organisms. They are used reiteratively in different tissues and stages, but the response of the receiving cells is controlled in a context dependent manner. The pattern of expression of the signalling molecule Wingless/WNT in Drosophila is extraordinarily complex. We have studied the mechanism that controls its expression and function in the outer ring of the Drosophila wing hinge. Our findings indicate that wingless expression is controlled by a dual mechanism: its initial activation requires the product of zinc finger homeodomain 2 and is subsequently repressed by the product of the gene complex elbow/no ocelli. This tight regulation restricts the activation of wingless temporally and spatially. Later in development, wingless expression is maintained by an autoregulatory loop that involves the product of homothorax. We have analyzed the phenotype of a wingless allelic combination that specifically removes the outer ring, and our results show that Wingless is required to promote local proliferation of the wing base cells. Thus, cell proliferation in the proximal-distal axis is controlled by the sequential activation of wingless in the inner ring and the outer ring at different stages of development.