Increasing control over biomineralization in conodont evolution.

Vertebrates use the phosphate mineral apatite in their skeletons, which allowed them to develop tissues such as enamel, characterized by an outstanding combination of hardness and elasticity. It has been hypothesized that the evolution of the earliest vertebrate skeletal tissues, found in the teeth of the extinct group of conodonts, was driven by adaptation to dental function. We test this hypothesis quantitatively and demonstrate that the crystallographic order increased throughout the early evolution of conodont teeth in parallel with morphological adaptation to food processing. With the c-axes of apatite crystals oriented perpendicular to the functional feeding surfaces, the strongest resistance to uniaxial compressional stress is conferred along the long axes of denticles. Our results support increasing control over biomineralization in the first skeletonized vertebrates and allow us to test models of functional morphology and material properties across conodont dental diversity.

Genome-scale exon perturbation screens uncover exons critical for cell fitness.

CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.

Enhanced Nesquehonite Formation and Stability in the Presence of Dissolved Silica.

One possible carbon dioxide sequestration strategy is via the carbonation of dissolved Mg2+ obtained through olivine ((Mg,Fe)2SiO4) dissolution. However, silica is also produced during the breakdown of olivine. This component may have a detrimental effect on the yield of Mg-carbonate as Mg2+ incorporation into complex Mg silicate phases would limit CO2 uptake by this system. Yet this potential competition is currently not considered. Here, we use crystal growth experiments at temperatures applicable for potential coastal applications to test the effect of silica on the formation of the hydrated Mg-carbonate phase nesquehonite (MgCO3·3H2O). Solution chemistry analysis coupled with phase identification demonstrates that the presence of silica in the solution can actually assist the formation of nesquehonite and increase its yield by as much as 60 times. Our findings suggest that the presence of silica changes interfacial stabilities, lowering the energetic barrier for nesquehonite nucleation. In addition, in situ attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) transformation experiments demonstrated that nesquehonite precipitating in a solution containing a high concentration of dissolved silica exhibits enhanced stability against its transformation into hydromagnesite. These findings will help to better constrain what we expect for applications of olivine during carbon remediation strategies as well as assist yields for industrial applications that use Mg-based cement as building materials to facilitate a CO2-neutral or negative footprint.

Mind the Interface Gap: Exposing Hidden Interface Defects at the Epitaxial Heterostructure between CuO and Cu2O.

Well designed and optimized epitaxial heterostructures lie at the foundation of materials development for photovoltaic, photocatalytic, and photoelectrochemistry applications. Heterostructure materials offer tunable control over charge separation and transport at the same time preventing recombination of photogenerated excitations at the interface. Thus, it is of paramount importance that a detailed understanding is developed as the basis for further optimization strategies and design. Oxides of copper are nontoxic, low cost, abundant materials with a straightforward and stable manufacturing process. However, in individual applications, they suffer from inefficient charge transport of photogenerated carriers. Hence, in this work, we investigate the role of the interface between epitaxially aligned CuO and Cu2O to explore the potential benefits of such an architecture for more efficient electron and hole transfer. The CuO/Cu2O heterojunction nature, stability, bonding mechanism, interface dipole, electronic structure, and band bending were rationalized using hybrid density functional theory calculations. New electronic states are identified at the interface itself, which are originating neither from lattice mismatch nor strained Cu-O bonds. They form as a result of a change in coordination environment of CuO surface Cu2+ cations and an electron transfer across the interface Cu1+-O bond. The first process creates occupied defect-like electronic states above the valence band, while the second leaves hole states below the conduction band. These are constitutional to the interface and are highly likely to contribute to recombination effects competing with the improved charged separation from the suitable band bending and alignment and thus would limit the expected output photocurrent and photovoltage. Finally, a favorable effect of interstitial oxygen defects has been shown to allow for band gap tunability at the interface but only to the point of the integral geometrical contact limit of the heterostructure itself.

Experimental and Theoretical Constraints on Amino Acid Formation from PAHs in Asteroidal Settings.

Amino acids and polycyclic aromatic hydrocarbons (PAHs) belong to the range of organic compounds detected in meteorites. In this study, we tested empirically and theoretically if PAHs are precursors for amino acids in carbonaceous chondrites, as previously suggested. We conducted experiments to synthesize amino acids from fluoranthene (PAH), with ammonium bicarbonate as a source for ammonia and carbon dioxide under mimicked asteroidal conditions. In our thermodynamic calculations, we extended our analysis to additional PAH-amino acid combinations. We explored 36 reactions involving the PAHs naphthalene, anthracene, fluoranthene, pyrene, triphenylene, and coronene and the amino acids glycine, alanine, valine, leucine, phenylalanine, and tyrosine. Our experiments do not show the formation of amino acids, whereas our theoretical results hint that PAHs could be precursors of amino acids in carbonaceous chondrites at low temperatures.

Magnetic structure and exchange interactions in pyrrhotite end member minerals: hexagonal FeS and monoclinic Fe7S8.

Iron mono-sulphides, or pyrrhotites, are minerals present in the Earth's crust and mantle as well as major magnetic constituents of several classes of meteorites, thus are of interest to a wide range of disciplines including geology, geophysics, geochemistry, and material science. Despite displaying diverse magnetic properties as a result of iron vacancy ordering, the underlying exchange mechanism has not been quantified. This study presents an examination of the electronic and magnetic properties for the two pyrrhotite group end members, hexagonal FeS and monoclinic Fe7S8(4C superstructure) by means of density functional theory coupled with a Heisenberg magnetic model. The easy magnetization axes of FeS and Fe7S8are found to be positioned along the crystallographicc-direction and at an angle of 56° to thec-direction, respectively. The magnetic anisotropy energy in Fe7S8is greatly increased as a consequence of the vacancy framework when compared to FeS. The main magnetic interaction, in both compounds, is found to be the isotropic exchange interaction favouring antiferromagnetic alignment between nearest-neighbouring spins. The origin of the exchange interaction is elucidated further following the Goodenough-Kanamori-Anderson rules. The antisymmetric spin exchange is found to have a minor effect in both compounds. The theoretical findings presented in this work thus help to further resolve some of the ambiguities in the magnetic features of pyrrhotites.

Influence of Inorganic Solution Components on Lithium Carbonate Crystal Growth.

Lithium-bearing brines are an increasingly attractive source of Li for extraction. One extraction mechanism is the removal of Li from the fluid phase through the precipitation of zabuyelite (Li2CO3). The chemistry of the brine plays an important role in this process because ions in solution can compete for the components of the Li-carbonate phase. Here we explore the effect of different brine components on the precipitation of zabuyelite using experiments and computational simulations. Crystals formed in all solutions showed morphological evidence for potential transformation from a precursor phase. Our study indicates that Ca2+ and SO4 2- are incorporated into the precipitated zabuyelite crystals. Sulfate also interacts directly with specific surfaces on the growing crystal and is expected to form ion pairs with Li+ in solution. Similarly, Na+ appears to form ion pairs in solution with the carbonate ion, slowing nucleation of zabuyelite in the experiments. K+ and Cl- may interact with the growing zabuyelite crystals but do not appear to affect zabuyelite nucleation and growth times. These experiments highlight the importance of understanding the solution chemistry on zabuyelite formation in order to predict the efficiency of extraction processes and the purity of the solids.

Correlative vibrational spectroscopy and 2D X-ray diffraction to probe the mineralization of bone in phosphate-deficient mice.

Bone crystallite chemistry and structure change during bone maturation. However, these properties of bone can also be affected by limited uptake of the chemical constituents of the mineral by the animal. This makes probing the effect of bone-mineralization-related diseases a complicated task. Here it is shown that the combination of vibrational spectroscopy with two-dimensional X-ray diffraction can provide unparalleled information on the changes in bone chemistry and structure associated with different bone pathologies (phosphate deficiency) and/or health conditions (pregnancy, lactation). Using a synergistic analytical approach, it was possible to trace the effect that changes in the remodelling regime have on the bone mineral chemistry and structure in normal and mineral-deficient (hypophosphatemic) mice. The results indicate that hypophosphatemic mice have increased bone remodelling, increased carbonate content and decreased crystallinity of the bone mineral, as well as increased misalignment of crystallites within the bone tissue. Pregnant and lactating mice that are normal and hypophosphatemic showed changes in the chemistry and misalignment of the apatite crystals that can be related to changes in remodelling rates associated with different calcium demand during pregnancy and lactation.

3D Raman Spectroscopy of Large Zeolite ZSM-5 Crystals.

Hydrothermal treatment is a common method used to modify the physicochemical properties of zeolite-based catalyst materials. It alters the number and type of acid sites through dealumination and increases molecular diffusion by mesopore formation. Steaming also reduces the structural integrity of zeolite frameworks. In this study, Raman microscopy has been used to map large zeolite ZSM-5 crystals before and after steaming. 3D elemental maps of T-O (T: Al or Si) sites of the zeolite were obtained. The Raman active vibrational bands were determined, which are indicative of (non-) framework Al, as well as of structural integrity. Zeolite steaming caused the introduction of additional heterogeneities within the zeolite framework. Al migration and the formation of extra-framework Al species were observed. The described experiments demonstrate the capability of 3D Raman spectroscopy as a valuable tool to obtain information on the spatial distributions of framework elements as well as defects within a zeolite-based material.

Sequestration of Antimony on Calcite Observed by Time-Resolved Nanoscale Imaging.

Antimony, which has damaging effects on the human body and the ecosystem, can be released into soils, ground-, and surface waters either from ore minerals that weather in near surface environments, or due to anthropogenic releases from waste rich in antimony, a component used in batteries, electronics, ammunitions, plastics, and many other industrial applications. Here, we show that dissolved Sb can interact with calcite, a widespread carbonate mineral, through a coupled dissolution-precipitation mechanism. The process is imaged in situ, at room temperature, at the nanometer scale by using an atomic force microscope equipped with a flow-through cell. Time-resolved imaging allowed following the coupled process of calcite dissolution, nucleation of precipitates at the calcite surface and growth of these precipitates. Sb(V) forms a precipitate, whereas Sb(III) needs to be oxidized to Sb(V) before being incorporated in the new phase. Scanning-electron microscopy and Raman spectroscopy allowed identification of the precipitates as two different calcium-antimony phases (Ca2Sb2O7). This coupled dissolution-precipitation process that occurs in a boundary layer at the calcite surface can sequester Sb as a solid phase on calcite, which has environmental implications as it may reduce the mobility of this hazardous compound in soils and groundwaters.

In Situ Nanoscale Investigation of Step Retreat on Fluoranthene Crystal Surfaces.

Fluoranthene, a polycyclic aromatic hydrocarbon, has been detected on Earth as well as in asteroids and meteorites and may have played a role in the formation of life. Increasing the ionic strength of aqueous solutions has been observed to lower the fluoranthene solubility, but it is unclear how solution composition controls the release rate of fluoranthene to an aqueous solution. To elucidate this, we performed in situ atomic force microscopy experiments in which we characterized the sublimation and dissolution behavior of fluoranthene crystal surfaces. From this, we quantify the step retreat rate upon exposure to air, deionized water, and a 0.4 M NaCl or 0.1 M MgSO4 solution. Surface roughness is the main factor that determines the dissolution or sublimation rate. The results imply that during fluoranthene remediation or breakdown in meteorites and asteroids, ionic strength will be more important than chemical composition for controlling fluoranthene release into solution.

Vibrational spectroscopic analysis of hydroxyapatite in HYP mice and individuals with X-linked hypophosphatemia.

BACKGROUND: X-linked hypophosphatemia (XLH) is the most common form of familial phosphate-wasting disorders, due to an inactivating mutation in the phosphate-regulating neutral endopeptidase, X-linked gene. Persistent osteomalacia, enthesophytes, osteophytes, degenerative arthritis and dental abscesses/periodontal disease dominate the adult disorder. However, the impact of insufficient phosphate on hydroxyapatite composition, the major inorganic component of bone and teeth, is unknown in individuals with XLH. METHODS: Using Raman spectroscopy, the carbonate (CO3 2-) to phosphate (PO4 3-) ion ratio was measured in HYP and wild-type mice and in primary and permanent teeth from XLH individuals and unaffected controls. RESULTS: There was a significant difference in carbonate ion substitution between the HYP and wild-type femoral cortical bone (0.36 ± 0.08 versus 0.24 ± 0.04; p < 0.001). Carbonate ion substitution levels were also higher in permanent XLH teeth compared with unaffected individuals (0.39 ± 0.12 versus 0.23 ± 0.04; p < 0.001), but not in primary teeth (0.29 ± 0.11 versus 0.26 ± 0.02; p = 0.29). Complementary Fourier transform infrared analyses demonstrated higher relative intensities of the four major vibrational bands originating from the carbonate anion in XLH teeth compared with unaffected controls. CONCLUSION: Ionic substitution within the crystal lattice is a common feature of hydroxyapatite and one that confers the physiological properties of bone that impact mechanical strength and the process of bone remodeling. Our data demonstrating anionic substitution in human dentin from individuals with XLH validate the use of dentin as a proxy for bone and to better understand the molecular adaptations that occur in the biochemical milieu of XLH.

Mineral Surface Rearrangement at High Temperatures: Implications for Extraterrestrial Mineral Grain Reactivity.

Mineral surfaces play a critical role in the solar nebula as a catalytic surface for chemical reactions and potentially acted as a source of water during Earth's accretion by the adsorption of water molecules to the surface of interplanetary dust particles. However, nothing is known about how mineral surfaces respond to short-lived thermal fluctuations that are below the melting temperature of the mineral. Here we show that mineral surfaces react and rearrange within minutes to changes in their local environment despite being far below their melting temperature. Polished surfaces of the rock and planetary dust-forming silicate mineral olivine ((Mg,Fe)2SiO4) show significant surface reorganization textures upon rapid heating resulting in surface features up to 40 nm in height observed after annealing at 1200 °C. Thus, high-temperature fluctuations should provide new and highly reactive sites for chemical reactions on nebula mineral particles. Our results also may help to explain discrepancies between short and long diffusion profiles in experiments where diffusion length scales are of the order of 100 nm or less.

Subduction zone forearc serpentinites as incubators for deep microbial life.

Serpentinization-fueled systems in the cool, hydrated forearc mantle of subduction zones may provide an environment that supports deep chemolithoautotrophic life. Here, we examine serpentinite clasts expelled from mud volcanoes above the Izu-Bonin-Mariana subduction zone forearc (Pacific Ocean) that contain complex organic matter and nanosized Ni-Fe alloys. Using time-of-flight secondary ion mass spectrometry and Raman spectroscopy, we determined that the organic matter consists of a mixture of aliphatic and aromatic compounds and functional groups such as amides. Although an abiotic or subduction slab-derived fluid origin cannot be excluded, the similarities between the molecular signatures identified in the clasts and those of bacteria-derived biopolymers from other serpentinizing systems hint at the possibility of deep microbial life within the forearc. To test this hypothesis, we coupled the currently known temperature limit for life, 122 °C, with a heat conduction model that predicts a potential depth limit for life within the forearc at ∼10,000 m below the seafloor. This is deeper than the 122 °C isotherm in known oceanic serpentinizing regions and an order of magnitude deeper than the downhole temperature at the serpentinized Atlantis Massif oceanic core complex, Mid-Atlantic Ridge. We suggest that the organic-rich serpentinites may be indicators for microbial life deep within or below the mud volcano. Thus, the hydrated forearc mantle may represent one of Earth's largest hidden microbial ecosystems. These types of protected ecosystems may have allowed the deep biosphere to thrive, despite violent phases during Earth's history such as the late heavy bombardment and global mass extinctions.

Imaging Organophosphate and Pyrophosphate Sequestration on Brucite by in Situ Atomic Force Microscopy.

In order to evaluate the organic phosphorus (OP) and pyrophosphate (PyroP) cycle and their fate in the environment, it is critical to understand the effects of mineral interfaces on the reactivity of adsorption and precipitation of OP and PyroP. Here, in situ atomic force microscopy (AFM) is used to directly observe the kinetics of coupled dissolution-precipitation on cleaved (001) surfaces of brucite [Mg(OH)2] in the presence of phytate, glucose-6-phosphate (G6P) and pyrophosphate, respectively. AFM results show that the relative order of contribution to mineral surface adsorption and precipitation is phytate > pyrophosphate > G6P under the same solution conditions and can be quantified by the induction time of OP/PyroP-Mg nucleation in a boundary layer at the brucite-water interface. Calculations of solution speciation during brucite dissolution in the presence of phytate or pyrophosphate at acidic pH conditions show that the solutions may reach supersaturation with respect to Mg5H2Phytate.6H2O as a Mg-phytate phase or Mg2P2O7 as a Mg-pyrophosphate phase that becomes thermodynamically stable before equilibrium with brucite is reached. This is consistent with AFM dynamic observations for the new phase formations on brucite. Direct nanoscale observations of the transformation of adsorption/complexation-surface precipitation, combined with spectroscopic characterizations and species simulations may improve the mechanistic understanding of organophosphate and pyrophosphate sequestration by mineral replacement reactions through a mechanism of coupled dissolution-precipitation occurring at mineral-solution interfaces in the environment.

Novel anatomic adaptation of cortical bone to meet increased mineral demands of reproduction.

The goal of this study was to investigate the effects of reproductive adaptations to mineral homeostasis on the skeleton in a mouse model of compromised mineral homeostasis compared to adaptations in control, unaffected mice. During pregnancy, maternal adaptations to high mineral demand include more than doubling intestinal calcium absorption by increasing calcitriol production. However, calcitriol biosynthesis is impaired in HYP mice, a murine model of X-linked hypophosphatemia (XLH). In addition, there is a paucity of mineralized trabecular bone, a primary target of bone resorption during pregnancy and lactation. Because the highest density of mineral is in mature cortical bone, we hypothesized that mineral demand is met by utilizing intracortical mineral reserves. Indeed, analysis of HYP mice revealed dramatic increases in intracortical porosity characterized by elevated serum PTH and type-I collagen matrix-degrading enzyme MMP-13. We discovered an increase in carbonate ion substitution in the bone mineral matrix during pregnancy and lactation of HYP mice, suggesting an alternative mechanism of bone remodeling that maintains maternal bone mass during periods of high mineral demand. This phenomenon is not restricted to XLH, as increased carbonate in the mineral matrix also occurred in wild-type mice during lactation. Taken together, these data suggest that increased intracortical perilacunar mineral turnover also contributes to maintaining phosphate levels during periods of high mineral demand. Understanding the mechanisms of skeletal contribution to mineral homeostasis is important to improving the treatment and prevention of fracture risk and bone fragility for female patients with XLH, but also provides important insight into the role and unique adaptations of the maternal skeleton to the demands of fetal development and the needs of postnatal nutrition.

Visualizing Organophosphate Precipitation at the Calcite-Water Interface by in Situ Atomic-Force Microscopy.

Esters of phosphoric acid constitute a large fraction of the total organic phosphorus (OP) in the soil environment and, thus, play an important role in the global phosphorus cycle. These esters, such as glucose-6-phosphate (G6P), exhibit unusual reactivity toward various mineral particles in soils, especially those containing calcite. Many important processes of OP transformation, including adsorption, hydrolysis, and precipitation, occur primarily at mineral-fluid interfaces, which ultimately governs the fate of organophosphates in the environment. However, little is known about the kinetics of specific mineral-surface-induced adsorption and precipitation of organophosphates. Here, by using in situ atomic-force microscopy (AFM) to visualize the dissolution of calcite (1014) faces, we show that the presence of G6P results in morphology changes of etch pits from the typical rhombohedral to a fan-shaped form. This can be explained by a site-selective mechanism of G6P-calcite surface interactions that stabilize the energetically unfavorable (0001) or (0112) faces through step-specific adsorption of G6P. Continuous dissolution at calcite (1014)-water interfaces caused a boundary layer at the calcite-water interface to become supersaturated with respect to a G6P-Ca phase that then drives the nucleation and growth of a G6P-Ca precipitate. Furthermore, after the introduction of the enzyme alkaline phosphatase (AP), the precipitates were observed to contain a mixture of components associated with G6P-Ca, amorphous calcium phosphate (ACP)-hydroxyapatite (HAP) and dicalcium phosphate dihydrate (DCPD). These direct dynamic observations of the transformation of adsorption- and complexation-surface precipitation and enzyme-mediated pathways may improve the mechanistic understanding of the mineral-interface-induced organophosphate sequestration in the soil environment.

Sequestration of selenium on calcite surfaces revealed by nanoscale imaging.

Calcite, a widespread natural mineral at the Earth's surface, is well-known for its capacity to sequester various elements within its structure. Among these elements, selenium is important because of its high toxicity in natural systems and for human health. In the form of selenite (Se((IV))), selenium can be incorporated into calcite during growth. Our in situ atomic force microscopy observations of calcite surfaces during contact with selenium-bearing solutions demonstrate that another process of selenium trapping can occur under conditions in which calcite dissolves. Upon the injection of solutions containing selenium in two states of oxidation (either Se((IV)) or Se((VI))), precipitates were observed forming while calcite was still dissolving. In the presence of selenate (Se((VI))), the precipitates formed remained small during the observation period. When injecting selenite (Se((IV))), the precipitates grew significantly and were identified as CaSeO3·H2O, based on SEM observations, Raman spectroscopy, and thermodynamic calculations. An interpretation is proposed where the dissolution of calcite increases the calcium concentration in a thin boundary layer in contact with the surface, allowing the precipitation of a selenium phase. This process of dissolution-precipitation provides a new mechanism for selenium sequestration and extends the range of thermodynamic conditions under which such a process is efficient.

Coupled dissolution and precipitation at the cerussite-phosphate solution interface: implications for immobilization of lead in soils.

In situ atomic force microscopy (AFM) has been used to study the interaction of phosphate-bearing solutions with cerussite, PbCO3, (010) surfaces. During the dissolution of cerussite we observed simultaneous growth of needle-shaped or spherical pyromorphite phases. This occurred at two different pH values and ionic strengths relevant to soil solution conditions. The initial dissolution processes occurring at the cerussite solid-phosphate solution interface were clearly distinguished, and heterogeneous nucleation and growth rates of pyromorphites at phosphate concentrations ranging from 0.1 µM to 10 mM were quantitatively defined. Enhanced cerussite dissolution in the presence of high salt (NaCl or NaF) concentrations leads to an increase in pyromorphite nucleation and growth rates. The newly formed pyromorphites were found to be stable upon contact with water or citrate-bearing solutions under acidic or alkaline conditions in the pH range 4-8. These in situ observations may improve the mechanistic understanding of processes resulting in lead immobilization in diverse soil systems as well as to enhance the effectiveness of phosphate-based treatments for remediation of lead-polluted soils.

Nanoscale observations of magnesite growth in chloride- and sulfate-rich solutions.

Magnesite growth in chloride and sulfate-rich solutions has been examined at 90 °C in situ using phase-shift interferometry (PSI) and ex situ using atomic force microscopy (AFM) to evaluate the feasibility of cosequestering SO2 and CO2 in Mg-rich rocks. Although sulfate may assist desolvation at the magnesite surface, evidence for enhanced growth was only found at specific surface sites. The overall growth rates fit with those observed for chloride experiments in similarly saturated solutions. Thus, the formation of Mg-SO4 ion pairs in solution, which lowers the supersaturation with respect to magnesite, will have the dominant effect during sequestration. Lowering the activity of Mg(2+) ions in solution also inhibited the nucleation of other hydrated Mg-carbonate phases. As no evidence was found for sulfate incorporation into the growing magnesite, the presence of sulfate in solution will be detrimental to CO2 sequestration and is not expected to be cosequestered. The PSI data also emphasize the variability of reactivity over the surface and how this changes as a function of solution saturation and composition.