Functional metagenomic screening identifies an unexpected ß-glucuronidase.

The abundance of recorded protein sequence data stands in contrast to the small number of experimentally verified functional annotation. Here we screened a million-membered metagenomic library at ultrahigh throughput in microfluidic droplets for ß-glucuronidase activity. We identified SN243, a genuine ß-glucuronidase with little homology to previously studied enzymes of this type, as a glycoside hydrolase 3 family member. This glycoside hydrolase family contains only one recently added ß-glucuronidase, showing that a functional metagenomic approach can shed light on assignments that are currently 'unpredictable' by bioinformatics. Kinetic analyses of SN243 characterized it as a promiscuous catalyst and structural analysis suggests regions of divergence from homologous glycoside hydrolase 3 members creating a wide-open active site. With a screening throughput of >107 library members per day, picolitre-volume microfluidic droplets enable functional assignments that complement current enzyme database dictionaries and provide bridgeheads for the annotation of unexplored sequence space.

Direct Observation of Enhanced Electron-Phonon Coupling in Copper Nanoparticles in the Warm-Dense Matter Regime.

Warm dense matter (WDM) represents a highly excited state that lies at the intersection of solids, plasmas, and liquids and that cannot be described by equilibrium theories. The transient nature of this state when created in a laboratory, as well as the difficulties in probing the strongly coupled interactions between the electrons and the ions, make it challenging to develop a complete understanding of matter in this regime. In this work, by exciting isolated ∼8 nm copper nanoparticles with a femtosecond laser below the ablation threshold, we create uniformly excited WDM. Using photoelectron spectroscopy, we measure the instantaneous electron temperature and extract the electron-ion coupling of the nanoparticle as it undergoes a solid-to-WDM phase transition. By comparing with state-of-the-art theories, we confirm that the superheated nanoparticles lie at the boundary between hot solids and plasmas, with associated strong electron-ion coupling. This is evidenced both by a fast energy loss of electrons to ions, and a strong modulation of the electron temperature induced by strong acoustic breathing modes that change the nanoparticle volume. This work demonstrates a new route for experimental exploration of the exotic properties of WDM.

Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data-model integration.

In an era of rapid global change, our ability to understand and predict Earth's natural systems is lagging behind our ability to monitor and measure changes in the biosphere. Bottlenecks to informing models with observations have reduced our capacity to fully exploit the growing volume and variety of available data. Here, we take a critical look at the information infrastructure that connects ecosystem modeling and measurement efforts, and propose a roadmap to community cyberinfrastructure development that can reduce the divisions between empirical research and modeling and accelerate the pace of discovery. A new era of data-model integration requires investment in accessible, scalable, and transparent tools that integrate the expertise of the whole community, including both modelers and empiricists. This roadmap focuses on five key opportunities for community tools: the underlying foundations of community cyberinfrastructure; data ingest; calibration of models to data; model-data benchmarking; and data assimilation and ecological forecasting. This community-driven approach is a key to meeting the pressing needs of science and society in the 21st century.

Assessment of yield gaps on global grazed-only permanent pasture using climate binning.

To meet rising demands for agricultural products, existing agricultural lands must either produce more or expand in area. Yield gaps (YGs)-the difference between current and potential yield of agricultural systems-indicate the ability to increase output while holding land area constant. Here, we assess YGs in global grazed-only permanent pasture lands using a climate binning approach. We create a snapshot of circa 2000 empirical yields for meat and milk production from cattle, sheep, and goats by sorting pastures into climate bins defined by total annual precipitation and growing degree-days. We then estimate YGs from intra-bin yield comparisons. We evaluate YG patterns across three FAO definitions of grazed livestock agroecosystems (arid, humid, and temperate), and groups of animal production systems that vary in animal types and animal products. For all subcategories of grazed-only permanent pasture assessed, we find potential to increase productivity several-fold over current levels. However, because productivity of grazed pasture systems is generally low, even large relative increases in yield translated to small absolute gains in global protein production. In our dataset, milk-focused production systems were found to be seven times as productive as meat-focused production systems regardless of animal type, while cattle were four times as productive as sheep and goats regardless of animal output type. Sustainable intensification of pasture is most promising for local development, where large relative increases in production can substantially increase incomes or "spare" large amounts of land for other uses. Our results motivate the need for further studies to target agroecological and economic limitations on productivity to improve YG estimates and identify sustainable pathways toward intensification.

Photo-ionization and fragmentation of Sc3N@C80 following excitation above the Sc K-edge.

We have investigated the ionization and fragmentation of a metallo-endohedral fullerene, Sc3N@C80, using ultrashort (10 fs) x-ray pulses. Following selective ionization of a Sc (1s) electron (hν = 4.55 keV), an Auger cascade leads predominantly to either a vibrationally cold multiply charged parent molecule or multifragmentation of the carbon cage following a phase transition. In contrast to previous studies, no intermediate regime of C2 evaporation from the carbon cage is observed. A time-delayed, hard x-ray pulse (hν = 5.0 keV) was used to attempt to probe the electron transfer dynamics between the encapsulated Sc species and the carbon cage. A small but significant change in the intensity of Sc-containing fragment ions and coincidence counts for a delay of 100 fs compared to 0 fs, as well as an increase in the yield of small carbon fragment ions, may be indicative of incomplete charge transfer from the carbon cage on the sub-100 fs time scale.

The role of protein dynamics in the evolution of new enzyme function.

Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.

Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles.

DNA-based computational hardware has attracted ever-growing attention due to its potential to be useful in the analysis of complex mixtures of biological markers. Here we report the design of self-assembling logic gates that recognize DNA inputs and assemble into crossover tiles when the output signal is high; the crossover structures disassemble to form separate DNA stands when the output is low. The output signal can be conveniently detected by fluorescence using a molecular beacon probe as a reporter. AND, NOT, and OR logic gates were designed. We demonstrate that the gates can connect to each other to produce other logic functions.

Nanodrawing of Aligned Single Carbon Nanotubes with a Nanopen.

Single-walled carbon nanotubes (SWCNTs) are considered pivotal components for molecular electronics. Techniques for SWCNT lithography today lack simplicity, flexibility, and speed of direct, oriented deposition at specific target locations. In this paper SWCNTs are directly drawn and placed with chemical identification and demonstrated orientation using fountain pen nanolithography (FPN) under ambient conditions. Placement across specific electrical contacts with such alignment is demonstrated and characterized. The fundamental basis of the drawing process with alignment has potential applications for other related systems such as inorganic nanotubes, polymers, and biological molecules.

Relative Photoionization Cross Sections of Super-Atom Molecular Orbitals (SAMOs) in C60.

The electronic structure and photoinduced dynamics of fullerenes, especially C60, is of great interest because these molecules are model systems for more complex molecules and nanomaterials. In this work we have used Rydberg Fingerprint Spectroscopy to determine the relative ionization intensities from excited SAMO (Rydberg-like) states in C60 as a function of laser wavelength. The relative ionization intensities are then compared to the ratio of the photoionization widths of the Rydberg-like states, computed in time-dependent density functional theory (TD-DFT). The agreement is remarkably good when the same photon order is required to energetically access the excited states. This illustrates the predictive potential of quantum chemistry for studying photoionization of large, complex molecules as well as confirming the assumption that is often made concerning the multiphoton excitation and rapid energy redistribution in the fullerenes.

Dynamics of thermal electron emission from highly excited C60.

Gas-phase fullerenes emit thermal electrons after femtosecond laser excitation in the wavelength range 400-800 nm. We have used angular-resolved photoelectron spectroscopy (PES) to study the influence of the laser's electric field on the dynamics of the thermally emitted electrons. The laser field introduces an asymmetry in the thermal electron distributions with respect to the laser polarization direction, which was confirmed by carrying out experiments at different wavelengths. A simple model could reproduce the trends in measured apparent temperatures in the PES. The asymmetry effect was exploited in a pump-probe experiment to estimate the time scale for thermal electron emission. It was found that, when 400 nm, 120 fs laser pulses of 2 TW cm(-2) intensity are used, thermal electrons are emitted up to ca. 300 fs after the peak of the laser pulse. The pump-probe scheme should be applicable to a wider range of complex molecules and clusters showing thermal electron emission on a femtosecond time scale.

Probing excited electronic states and ionisation mechanisms of fullerenes.

Fullerenes are interesting model systems for probing the complex, fundamental electron dynamics and ionisation mechanisms of large molecules and nanoparticles. In this Tutorial Review we explain how recent experimental and theoretical advances are providing insight into the interesting phenomenon of thermal electron emission from molecular systems and the properties of hydrogenic, diffuse, excited electronic states, known as superatom molecular orbitals, which are responsible for relatively simple, well-resolved structure in fs laser photoelectron spectra of fullerenes. We focus on the application of velocity map imaging combined with fs laser photoionisation to study angular-resolved photoelectron emission.

Electromechanically tunable carbon nanofiber photonic crystal.

We demonstrate an electrically tunable 2D photonic crystal array constructed from vertically aligned carbon nanofibers. The nanofibers are actuated by applying a voltage between adjacent carbon nanofiber pairs grown directly on metal electrodes, thus dynamically changing the form factor of the photonic crystal lattice. The change in optical properties is characterized using optical diffraction and ellipsometry. The experimental results are shown to be in agreement with theoretical predictions and provide a proof-of-principle for rapidly switchable photonic crystals operating in the visible that can be fabricated using standard nanolithography techniques combined with plasma CVD growth of the nanofibers.

Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase.

Lanthanide ions have ideal chemical properties for catalysis, such as hard Lewis acidity, fast ligand-exchange kinetics, high coordination-number preferences and low geometric requirements for coordination. As a result, many small-molecule lanthanide catalysts have been described in the literature. Yet, despite the ability of enzymes to catalyse highly stereoselective reactions under gentle conditions, very few lanthanoenzymes have been investigated. In this work, the mononuclear binding of europium(III) and gadolinium(III) to the active site of a mutant of the model enzyme phosphotriesterase are described using X-ray crystallography at 1.78 and 1.61 Šresolution, respectively. It is also shown that despite coordinating a single non-natural metal cation, the PTE-R18 mutant is still able to maintain esterase activity.

Carbon savings from sugarcane-straw derived bioenergy: Insights from a life cycle perspective including soil carbon changes.

Sugarcane straw removal for bioenergy production will increase substantially in the next years, but this may deplete soil organic carbon (SOC) and exacerbate greenhouse gas (GHG) emissions. These aspects are not consistently approached in bioenergy life cycle assessment (LCA). Using SOC modeling and LCA approach, this study addressed the life cycle GHG balance from sugarcane agroindustry in different scenarios of straw removal, considering the potential SOC changes associated with straw management in sugarcane-cultivated soils in Brazil. Long-term simulations showed SOC losses of up to -0.5 Mg ha-1 yr-1 upon complete straw removal, whereas the moderate removal had little effects on SOC and the maintenance of all straw in the field increased SOC accumulation by up to 0.4 Mg ha-1 yr-1. Our analysis suggests that accounting for SOC changes in LCA calculations could lower the net GHG benefits of straw-derived bioenergy, whose emissions intensity varied according to soil type. Overall, SOC depletion induced by complete straw removal increased the life cycle GHG emissions of straw-derived bioenergy by 26 % (3.9 g CO2eq MJ-1) compared to a scenario without taking SOC changes into account. Straw removal for cellulosic ethanol could be effective for mitigating GHG emissions relative to gasoline, but it was not advantageous for bioelectricity generation depending on the energy sources that are displaced. Therefore, straw-induced change of SOC stocks is a critical factor to model life cycle GHG emissions of straw-derived bioenergy.

Probing rapidly-ionizing super-atom molecular orbitals in C60: a computational and femtosecond photoelectron spectroscopy study.

Super-atom molecular orbitals (SAMOs) are diffuse hydrogen-like orbitals defined by the shallow potential at the centre of hollow molecules such as fullerenes. The SAMO excited states differ from the Rydberg states by the significant electronic density present inside the carbon cage. We provide a detailed computational study of SAMO and Rydberg states and an experimental characterization of SAMO excited electronic states for gas-phase C(60) molecules by photoelectron spectroscopy. A large band of 500 excited states was computed using time-dependent density functional theory. We show that due to their diffuse character, the photoionization widths of the SAMO and Rydberg states are orders of magnitude larger than those of the isoenergetic non-SAMO excited states. Moreover, in the range of kinetic energies experimentally measured, only the SAMO states photoionize significantly on the timescale of the femtosecond laser experiments. Single photon ionization of the SAMO states dominates the photoelectron spectrum for relatively low laser intensities. The computed photoelectron spectra and photoelectron angular distributions are in good agreement with the experimental results.

Hot electron production and diffuse excited states in C70, C82, and Sc3N@C80 characterized by angular-resolved photoelectron spectroscopy.

Angular-resolved photoelectron spectroscopy using wavelength-tuneable femtosecond laser pulses is presented for a series of fullerenes, namely, C70, C82, and Sc3N@C80. The photoelectron kinetic energy distributions for the three molecules show typical thermal electron spectra with a superimposed peak structure that is the result of one-photon ionization of diffuse low-angular momenta states with electron density close to the carbon cage and that are related to so-called super atom molecular orbitals. Photoelectron angular distributions confirm this assignment. The observed structure is less prominent compared to the thermal electron background than what was observed in C60. It can be concluded that hot electron emission is the main ionization channel for the larger and more complex molecules for these excitation conditions.

Determination of the bending rigidity of graphene via electrostatic actuation of buckled membranes.

Classical continuum mechanics is used extensively to predict the properties of nanoscale materials such as graphene. The bending rigidity, κ, is an important parameter that is used, for example, to predict the performance of graphene nanoelectromechanical devices and also ripple formation. Despite its importance, there is a large spread in the theoretical predictions of κ for few-layer graphene. We have used the snap-through behavior of convex buckled graphene membranes under the application of electrostatic pressure to determine experimentally values of κ for double-layer graphene membranes. We demonstrate how to prepare convex-buckled suspended graphene ribbons and fully clamped suspended membranes and show how the determination of the curvature of the membranes and the critical snap-through voltage, using AFM, allows us to extract κ. The bending rigidity of bilayer graphene membranes under ambient conditions was determined to be 35.5−15.0 +20.0 eV. Monolayers are shown to have significantly lower κ than bilayers.

Cytochrome P450-catalyzed oxidation of halogen-containing substrates.

Cytochrome P450 (CYP) enzymes are heme-thiolate monooxygenases which catalyze the oxidation of aliphatic and aromatic C-H bonds and other reactions. The oxidation of halogens by cytochrome P450 enzymes has also been reported. Here we use CYP199A4, from the bacterium Rhodopseudomonas palustris strain HaA2, with a range of para-substituted benzoic acid ligands, which contain halogens, to assess if this enzyme can oxidize these species or if the presence of these electronegative atoms can alter the outcome of P450-catalyzed reactions. Despite binding to the enzyme, there was no detectable oxidation of any of the 4-halobenzoic acids. CYP199A4 was, however, able to efficiently catalyze the oxidation of both 4-chloromethyl- and 4-bromomethyl-benzoic acid to 4-formylbenzoic acid via hydroxylation of the α­carbon. The 4-chloromethyl substrate bound in the enzyme active site in a similar manner to 4-ethylbenzoic acid. This places the benzylic α­carbon hydrogens in an unfavorable position for abstraction indicating a degree of substrate mobility must be possible within the active site. CYP199A4 catalyzed oxidations of 4-(2'-haloethyl)benzoic acids yielding α-hydroxylation and desaturation metabolites. The α-hydroxylation product was the major metabolite. The desaturation pathway is significantly disfavored compared to 4-ethylbenzoic acid. This may be due to the electron-withdrawing halogen atom or a different positioning of the substrate within the active site. The latter was demonstrated by the X-ray crystal structures of CYP199A4 with these substrates. Overall, the presence of a halogen atom positioned close to the heme iron can alter the binding orientation and outcomes of enzyme-catalyzed oxidation.

Angular-resolved photoelectron spectroscopy of superatom orbitals of fullerenes.

Photoelectron angular distributions from both C(60) and C(70) were recorded for low laser intensity femtosecond and picosecond pulses. Rich structure is seen for electron kinetic energies that lie below the photon energy. Strong, broad peaks are observed for photoelectron energies corresponding to single-photon ionization of so-called superatom molecular orbitals (SAMOs). The very simple angular distributions measured for these peaks, the close similarity of the spectra observed from C(60) and C(70), and the comparison with time-dependent density functional theory provide strong support for the SAMO hypothesis.