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Genetic and Antigenic Characterization of an Expanding H3 Influenza A Virus Clade in U.S. Swine Visualized by Nextstrain
Defining factors that influence spatial and temporal patterns of influenza A virus (IAV) is essential to inform vaccine strain selection and strategies to reduce the spread of potentially zoonotic swine-origin IAV. The relative frequency of detection of the H3 phylogenetic clade 1990.4.a (colloquially known as C-IVA) in U.S. swine declined to 7% in 2017 but increased to 32% in 2019. We conducted phylogenetic and phenotypic analyses to determine putative mechanisms associated with increased detection. We created an implementation of Nextstrain to visualize the emergence, spatial spread, and genetic evolution of H3 IAV in swine, identifying two C-IVA clades that emerged in 2017 and cocirculated in multiple U.S. states. Phylodynamic analysis of the hemagglutinin (HA) gene documented low relative genetic diversity from 2017 to 2019, suggesting clonal expansion. The major H3 C-IVA clade contained an N156H amino acid substitution, but hemagglutination inhibition (HI) assays demonstrated no significant antigenic drift. The minor HA clade was paired with the neuraminidase (NA) clade N2-2002B prior to 2016 but acquired and maintained an N2-2002A in 2016, resulting in a loss of antigenic cross-reactivity between N2-2002B- and -2002A-containing H3N2 strains. The major C-IVA clade viruses acquired a nucleoprotein (NP) of the H1N1pdm09 lineage through reassortment in the replacement of the North American swine-lineage NP. Instead of genetic or antigenic diversity within the C-IVA HA, our data suggest that population immunity to H3 2010.1 along with the antigenic diversity of the NA and the acquisition of the H1N1pdm09 NP gene likely explain the reemergence and transmission of C-IVA H3N2 in swine.
Computational Discovery of Ultralow Thermal Conductivity in the Energy-Degenerate Polymorphic Crystal Family A 2 M 2 M’Q 4
Crystalline materials, characterized by their well-defined lattices, typically exhibit a unique global thermodynamic minimum for a specific composition. However, in this study, we discover a quaternary chalcogenide family, A 2 M 2 M’Q 4 (A: alkali metals; M: coinage metal; M’: transition or group-IVA metals; Q: chalcogens), that exhibits pervasive energy (near-)degeneracy. For a given composition, multiple structurally distinct polymorphs exist within a formation enthalpy window of only a few milli-electron volts per atom. We quantify this inherent structural flexibility using a dedicated descriptor, σ f : the standard deviation of formation enthalpies among degenerate (meta)stable polymorphs. The consistently low σf observed across the A 2 M 2 M’Q 4 family signifies a characteristically shallow and frustrated potential energy landscape, which drives pronounced lattice anharmonicity, marking these materials as prime candidates for ultralow lattice thermal conductivity (κ L ). Employing an advanced high-throughput computational framework that integrates thermodynamics, lattice dynamics, and thermal conductivity calculations, we screen 1215 A 2 M 2 M’Q 4 compounds, identifying 30 stable candidates with κ L < 0.5 W m –1 K –1 at 300 K. Among them, Rb 2 Ag 2 SnTe 4 and Rb 2 Au 2 HfTe 4 , two representatives from the IVA and TM subgroups, are predicted to show ultralow room-temperature κ L of 0.174 W m –1 K –1 and 0.295 W m –1 K –1 , respectively. A systematic analysis suggests that the nonbonding and antibonding states induced by “dual rattlers” are the origin of low thermal conductivity in these compounds. Our results position the A 2 M 2 M’Q 4 family as a rich source of intrinsic thermal insulators and suggest that polymorphic energy degeneracy may serve as a valuable signpost for identifying crystalline families with potential anharmonicity.
Characterization of self-magnetic pinch radiographic diode performance on RITS-6 at Sandia National Laboratories. II. Coupling between the inductive voltage adder and the SMP load
The self-magnetic pinch (SMP) diode is a type of radiographic diode used to generate an intense electron beam for radiographic applications. At Sandia National Laboratories, SMP was the diode load for the six-cavity radiographic integrated test stand inductive voltage adder (IVA) driver operated in a magnetically insulated transmission line (MITL). The MITL contributes a flow current in addition to the current generated within the diode itself. Extensive experiments with a MITL of 40Ω load impedance [T. J. Renk et al., Phys. Plasmas 29, 023105 (2022)] indicate that the additional flow current leads to results similar to what might be expected from a conventional high-voltage interface driver, where flow current is not present. However, when the MITL flow impedance was increased to 80 Ω, qualitatively different diode behavior was observed. This includes large retrapping waves suggestive of an initial coupling to low impedance as well as diode current decreasing with time even as the total current does not. A key observation is that the driver generates total current (flow + diode) consistent with the flow impedance of the MITL used. The case is made in this paper that the 80Ω MITL experiments detailed here can only be understood when the IVA-MITL-SMP diode is considered as a total system. Additionally, the constraint of fixed total current plus the relatively high flow impedance limits the ability of the diode (whether SMP or other type) to act as an independent load. An unexpected new result is that in tracking the behavior of the electron strike angle on the converter as a function of time, we observed that the conventional cIV x “Radiographic” radiation scaling (where x~2.2) begins to break down for voltages above 8 MV, and cubic scaling is required to recover accurate angle tracking.
Characterization of Self-Magnetic Pinch (SMP) Radiographic Diode Performance on RITS-6 at Sandia National Laboratories
The goals of an electron beam-driven radiographic source are the focusing of high current at high voltage to a minimal spot size with excellent shot-to-shot reproducibility. The Self-Magnetic Pinch (SMP) diode makes use of such an intense electron beam impinging on a high-atomic weight (tantalum) converter, a counter-streaming ion beam to help minimize the spot size, and operation in a magnetic field-free diode region which further encourages small spot size. Through a series of diode development experiments, output voltages up to 12.5 MV and output currents up to 225 kA have been characterized, with resulting spot sizes below ~ few mm. Scaling studies with parameter variation, such as diode aspect ratio and anode-cathode (A-K) gap variation, give systematic validation to what has heretofore been noted anecdotally by other research groups. While the lack of an imbedded magnetic field helps minimize the SMP spot size, a secondary result may be the generation of beam instabilities which can terminate the radiation pulse. There is anecdotal evidence that in-situ DC heating of the diode region can help stabilize the beam pinch. Clear experimental evidence exists that DC heating/RF cleaning results in better control over the counter-streaming ion population. Expanded use of spatial dose-rate detection is shown to yield new insights into electron beam dynamics in the SMP diode. An attendant study of the SMP diode as a load for an Inductive Voltage Adder (IVA) driver leads to insights into the behavior of the IVA-SMP diode configuration, viewed as a total system, and yields constraints on the overall impedance behavior of the SMP diode load.
Bleach Rescues Nannochloropsis from an Obligate Parasite and Alters Microbial and Metabolite Signatures of Outdoor Cultures
Chemical agents are commonly used to protect algal crops. Yet, few studies have characterized the effects of these agents on associated microbial communities to understand effects on microbial functions relevant to algal crop production and protection. Here, we used shotgun metagenomic sequencing and untargeted exometabolite profiling to link the application of bleach, a -cidal agent used to protect algae from pests, to changes in community composition, metabolic pathways, and exometabolies - at a whole community level. Bleach protected the algal crop from crashing but altered bacterial diversity. Analysis of metagenome-assembled genomes (MAGs) revealed a classic predator-prey cycle between Oligoflexus and our target alga Nannochloropsis. Olifoflexus genomes from our study were notably similar to a previously identified BALO (Bdellovibrio and like organism), FD111, known to kill Nannochloropsis cultures, providing strong evidence that an FD111-like organism was responsible for the crash. Metabolic pathway composition differed between bleached and unbleached ponds, with abundance of twelve pathways related to stress tolerance, including the superpathway of methylglyoxal degradation, lipid IVA biosynthesis, and ectoine biosynthesis, greater in bleached ponds compared to unbleached ponds. Virulence factors related to adherence, biofilm formation, motility, and pathogenicity increased dramatically in bleached ponds with time, although this increase was not coupled with an increase in pathogens - algal or otherwise - or a decline in algal health. Our study highlights the importance of coupling 16S rRNA gene sequencing with whole genome data and other -omics tools to sketch a larger picture of community structure and function in crop systems. Moreover, our results highlight that continued long-term bleaching may lead to negative effects to crop health or downstream adverse health effects to humans or animals, depending on the algal product (i.e. human supplements or animal feedstocks). Future work on alternative treatment methods that would reduce resistance is necessary in the field.
Data on Cu- and Ni-Si-Mn-rich solute clustering in a neutron irradiated austenitic stainless steel
The data presented in this article is supplementary to the research article “Phase instabilities in austenitic steels during particle bombardment at high and low dose rates” (Levine et al.). Needle-shaped samples were prepared with focused ion beam milling from a 304L stainless steel that was irradiated with fast neutrons (E 0.1 MeV) in the BOR-60 reactor at 318 °C to 47.5 dpa. Atom probe tomography (APT) experiments in voltage mode were then conducted on a Cameca LEAP 5000X HR. Atom position, range, and mass spectrum files after reconstruction with Cameca’s IVAS software are included. Cu- and Ni-Si-Mn-rich solute nanoclusters were identified and analyzed using the Open Source Characterization of APT Reconstructions (OSCAR) program. Python code for OSCAR, information on the program’s underlying algorithm, and sample output files are provided. A proximity histogram of a Ni-Si-Mn-rich cluster and a 1D density/solute concentration profile of a Cu-rich cluster are given to demonstrate OSCAR’s analytical functionalities. The provided APT dataset is valuable for benchmarking phase instabilities in neutron-irradiated austenitic stainless steels that occur at high doses. The OSCAR program can be reused to process other APT data sets where solute nanoclustering is of interest.
Chemical characteristics of iron meteorite parent bodies
The projected relative abundances of the highly siderophile elements (HSE; Re, Os, Ir, Ru, Pt, and Pd) for bulk parent bodies of 10 magmatic iron meteorite groups/grouplet (IC, IIAB, IIC, IID, IIF, IIIAB, IIIF, IVA, IVB, and South Byron Trio) are broadly similar and show no resolvable differences between noncarbonaceous (NC) and carbonaceous (CC) genetic heritage. The processes driving genetic isotopic heterogeneity in the early Solar System, therefore, evidently did not leave discernable chemical fingerprints with respect to HSE relative abundances on the bulk planetesimal scale. By contrast, the absolute abundances of HSE projected for parent body cores, which reflect core size, are more variable and, on average, higher in CC bodies compared to NC bodies. Overall, bulk core chemical compositions, as well as core size, are linked to the distribution of Fe within a parent body, which is controlled by its oxidation state. The CC parent bodies are constrained to have formed under heterogeneous oxidizing conditions which were, on average, more oxidizing than those of the NC environment.
Extensively Microtwinned Diamond with Nanolaminates of Lonsdaleite Formed by Flash Laser Heating of Glassy Carbon
Diamond’s unique properties on the nanoscale make it one of the most important materials for use in biosensors and quantum computing and for components that can withstand the harsh environments of space. We synthesize oriented, faceted diamond particles by flash laser heating of glassy carbon at 16 GPa and 2300 K. Detailed transmission electron microscopy shows them to consist of a mosaic of diamond nanocrystals frequently joined at twin boundaries forming microtwins. Striking 3-fold translational periodicity was observed in both imaging and diffraction. This periodicity was shown to originate from nanodimensional wedge-shaped overlapping regions of twinned diamond and not from a possible 9R polytype, which has also been reported in other group IVa elements and water ice. Extended bilayers of hexagonal layer stacking were observed, forming lonsdaleite nanolaminates. In conclusion, the particles exhibited optical fluorescence with a rapid quench time (<1 ns) attributed to their unique twinned microstructure.
Encapsulation in a Bacterial Microcompartment Shell Improves Thermal Stability of a Glycolytic Enzyme
Selective encapsulation of target enzymes is an increasingly well-studied field, with a host of potential applications for biotechnology. Natively, many bacteria utilize bacterial microcompartments (BMCs) for enzyme encapsulation to enhance catalysis. BMCs are protein shells that enable selective localization of targeted metabolic enzymes and may improve catalytic rates by colocalizing pathway enzymes and/or serve to sequester toxic or volatile intermediates. The microcompartment shell of Haliangium ochraceum (HO) is a notable BMC chassis because of its modularity and versatility; it is easily expressed and assembled outside its native host and can accept a wide array of cargo. Recently, it was demonstrated that assembly of HO BMC shells can be easily achieved in vitro. Following up on our previous work on in vivo assembly of HO-BMCs with triose phosphate isomerase (TPI) as a model enzyme cargo, here we have demonstrated the advantages of in vitro assembly (IVA) for targeted enzyme encapsulation. We achieved variable loading of BMC shells with targeted amounts of TPI and demonstrated enhanced thermal stability of encapsulated TPI versus free TPI up to 62 °C.
Characterization of Self-Magnetic Pinch (SMP) radiographic diode performance on RITS-6 at Sandia National Laboratories: 1) Diode Dynamics, DC Heating to extend Radiation Pulse
Radiographic diodes focus an intense electron beam to a small spot size to minimize the source area of energetic photons for radiographic interrogation. The self-magnetic pinch (SMP) diode has been developed as such a source and operated as a load for the RITS-6 Inductive Voltage Adder (IVA) driver. While experiments support the generally accepted conclusion that a 1:1 aspect diode (cathode diameter equals anode-cathode gap) delivers optimum SMP performance, such experiments also show that reducing the cathode diameter, while reducing spot size, also results in reduced radiation dose, by as much as 50%, and degraded shot reproducibility. Analyzation of the effective electron impingement angle on the anode converter with time made possible by a newly developed dose-rate array diagnostic indicates that fast-developing oscillations of the angle are correlated with early termination of the radiation pulse on many of the smaller-diameter SMP shots. This behavior as a function of relative cathode size persists through experiments with output voltages and currents up to 11.5 MV and 225 kA, respectively, and with spot sizes below ~ few mm. Since simulations to date have not predicted such oscillatory behavior, considerable discussion of the angle-behavior of SMP shots is made to lend credence to the inference. There is clear anecdotal evidence that DC heating of the SMP diode region leads to stabilization of this oscillatory behavior. This is the first of two papers on the performance of the SMP diode on the RITS-6 accelerator.
Design of protein-binding proteins from the target structure alone
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder–target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein–protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
Role of Wadsley Defects and Cation Disorder to Enhance MoNb 12 O 33 Diffusion
Wadsley-Roth (WR) niobates have emerged as high-rate anode materials that can combine rapid ionic diffusion with good electronic conductivity. WR compounds have been defect-enhanced by limited annealing, however, such materials often contain multiple types of defects. In particular, both Wadsley defects (variable block size) and transition metal disorder have the potential to modify transport rates, however the corresponding effects are not well understood mechanistically. Here, MoNb 12 O 33 (MNO) was calcined at two different temperatures to compare a defect-rich condition (MNO-800) with a proximal order-rich condition (MNO-900) as assessed through XRD, XANES, EXAFS, and STEM characterizations. Galvanostatically cycled lithium half cells of MNO-800 exhibited additional capacity (307 mAhg −1 at 0.1C, 4.66% higher) and improved high-rate capacity of 200 mAhg −1 at 10C. ICI-based overpotential analysis identified solid state diffusion as the dominant rate limiting process where MNO-800 correspondingly exhibited ∼3X faster capacity-weighted diffusivity. A machine-learning interatomic potential was trained to density functional theory and then applied with molecular dynamics (MLIP-MD) to examine the possible roles of Wadsley defects and transition metal disorder. For both defect-types, Li was found to populate and activate fast diffusion paths from window sites at lower extents of lithiation as compared to the order-rich model.
Crystal structures of inhibitor complexes of M‐PMV protease with visible flap loops
Abstract Mason‐Pfizer monkey virus protease (PR) was crystallized in complex with two pepstatin‐based inhibitors in P 1 space group. In both crystal structures, the extended flap loops that lock the inhibitor/substrate over the active site, are visible in the electron density either completely or with only small gaps, providing the first observation of the conformation of the flap loops in dimeric complex form of this retropepsin. The H‐bond network in the active site (with D26N mutation) differs from that reported for the P 2 1 crystal structures and is similar to a rarely occurring system in HIV‐1 PR.
Nitrogen-doped char as a catalyst for wet oxidation of phenol-contaminated water
Catalytic wet oxidation (CWO) of aqueous effluents rich in organic compounds is a very promising technology for the treatment of liquid wastes from biomass conversion processes. CWO reactions occur through the formation of free radical species, produced in the presence of an oxidant, which act on organic contaminates in the effluent. Although the reaction is well known, there exists a lack of affordable catalysts to conduct this process at the lower temperatures and pressures in novel bioenergy processes. Here, this study assessed the catalytic effect of nitrogen-doped chars as such an option. Phenol in aqueous solution was used as a model waste effluent. Treatment was conducted at moderate temperatures (190 to 260 °C), oxygen partial pressure of 1 MPa, and reaction times of 15, 30, and 45 min in stainless steel and glass-lined tube reactors. High pressure liquid chromatography (HPLC) analyses of the products quantified phenol and by-product concentrations used in the calculation of reaction activation energy. The char catalyst was studied by X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) in order to gain insight into its structure and surface composition. The results indicate that nitrogen-doped char catalysts accelerate the oxidation of phenol by decreasing its reaction activation energy from 82.2 kJ/mol (non-catalyzed) to 40.4 kJ/mol (catalyzed). An analysis from first principles using density functional theory (DFT) was conducted to ascertain which N functional group has the most significant impact on free radical formation in the presence of oxygen. Among all the N functional groups studied, the dipyridinic functional groups showed the most promising characteristics to facilitate the formation of hydroxyl free radicals.
Thermal stability and protective properties of phenylphosphonic acid on Cu(111)
Phenylphosphonic acid (PPA) adsorbed on Cu(111) has been studied by synchrotron radiation-based techniques in combination with density functional theory calculations. Here, the dehydrogenated phenylphosphonic acid molecule (PP) strongly bound in a tridentate geometry through oxygen atoms to Cu(111) is shown to be the dominant surface species in the temperature range 150–300 °C. The stable PP adlayer substantially protects the Cu(111) surface from oxidation during exposure to ambient conditions. Thermal treatment of the PPA adlayer at 375 °C initiates molecular decomposition through several channels: P–O bond scission forming C 6 H 5 PO 2 ; C–P bond scission forming phenyl and PO 3 ; and C–H bond scission forming C 6 H 4 PO 3 . All three reaction steps have activation barriers of 1.7–1.8 eV. Small products such as O, H, and phenyl can immediately react further and desorb, while the remaining phosphonate species undergo condensation. After annealing at a higher temperature, the phosphonate group is further reduced from oxygen-rich to phosphorus-rich species, which form the majority of remaining adsorbates after 500 °C treatment.
Biogeochemical Controls on Wood Degradation as a Source of Bioavailable Carbon in Denitrifying Bioreactors
Woodchip bioreactors (WBRs) are important tools for the removal of nitrate in agricultural drainage, but their effectiveness is often limited by the slow degradation of lignocellulosic wood residues into bioavailable forms of carbon that fuel denitrifying microorganisms. Here, we examine biogeochemical factors regulating wood degradation in saturated woodchip beds, with a focus on the effects of dissolved oxygen (DO), iron (Fe), and manganese (Mn) in generating oxidative activity that can enhance wood decomposition. Woodchips from a 10-year-old WBR were characterized with bulk techniques and a novel combination of μX-ray scattering, μXRF, and μXANES to visualize the depletion of crystalline cellulose as a proxy for wood degradation. Woodchips from upstream portions of the reactor exhibited the greatest degradation, probably due to greater DO exposure, and degradation was localized to a 100 to 200 μm thick surface layer that was also associated with higher concentrations of Fe and Mn. Greater degradation was associated with faster nitrate removal. μXANES analysis of Fe and Mn in the surface layer indicated the presence of a microenvironment in which oxygenation reactions of Fe(II) and Mn(II) could contribute to the formation of reactive oxidants involved in the degradation of lignocellulose. In conclusion, our results provide new insight into biogeochemical properties that influence wood decomposition in WBRs at both micro- and macroscales and how these wood degradation processes are coupled with denitrification.