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At least 181 records · Page 10

Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer

The degradation of organic matter (OM) by microorganisms in thawing permafrost produces greenhouse gases. Terrestrial OM is transported into fjords through hydrological runoff, but it is unclear whether the microbial mechanisms of OM degradation on land persist after soils enter marine environments, which differ greatly in conditions and microbial communities. This question is particularly relevant for low-OM soils, which dominate Arctic landscapes and are more exposed to oxidants. Here, we compared OM-degrading capacity in permafrost-affected active layer soils and adjacent fjord sediments from Kongsfjorden, Svalbard, focusing on carbohydrate-active enzymes (CAZymes), which target some of the most abundant types of organic matter in soils. Using multi-omics approaches—metagenomics, metagenome-assembled genomes (MAGs), metabolomics, metatranscriptomics, and metaproteomics—we examined CAZyme presence, distribution, and activity. Despite environmental differences, both soils and sediments harbored diverse glycoside hydrolases and polysaccharide lyases, most of which showed evidence of activity. Verrucomicrobia expressed the highest number of CAZyme transcripts, indicating that they dominated active carbohydrate degradation in fjord sediments, while Acidobacteria and Actinobacteria were more active in soils. Notably, CAZymes in fjord sediments targeted primarily soil-derived OM, and the proportions of enzymes degrading terrestrial OM, marine OM, and microbial necromass—remnants of dead microbial cells were similar across both environments. These results suggest that microbial communities in both soils and fjord sediments are equipped to degrade carbohydrates, and that burial of terrestrial-derived OM in fjord sediments may not protect it from microbial breakdown under Arctic warming.

Chukwufumnanya, Abuah [University of Tennessee, Kn↗

Revealing Hidden Quinones Through Diagnostic MS² Fragmentation of Peptide–Quinone Adducts

Quinones are redox-active components of natural organic matter that mediate electron transfer and influence biogeochemical processes, but many quinones in pyrogenic organic matter (PyOM) remain unresolved because they ionize poorly by mass spectrometry. Here, we present a peptide-tagging approach to improve detection of cysteine-reactive electrophiles in PyOM, with quinones expected to be a dominant subset based on reaction chemistry and selectivity experiments. A cysteine-containing peptide was used to form Michael-addition adducts, enhancing electrospray ionization and enabling untargeted screening by high-performance liquid chromatography-high-resolution tandem mass spectrometry. The method was benchmarked with five quinone standards and applied to extracts from charred plant material as a discovery-level screen for cysteine-reactive targets. We identified 98 quinone-candidate adducts (mean neutral mass ~603 Da), of which more than 70% were not detectable in native MS1 data. Among formula-assigned features, hidden quinone candidates had median (O+N)/C of 0.391 and normalized oxidation state of carbon of -0.281, consistent with relatively low polarity and low oxidation state. These results reveal a previously inaccessible pool of hidden redox-active compounds in PyOM and provide a framework for prioritizing quinone-like electrophiles for confirmation and incorporation into models of fire-driven biogeochemical cycling.

LC-MS/MS↗

Extraction of an urease-active organo-complex from soil.

Description of an extraction from a Dublin clay loam soil of a colloidal organic matter complex that is urease active and, by X-ray analysis, free of clays. Urease activity in the clay-free precipitates, as in the soil, was not destroyed by the activity of an added proteolytic enzyme, pronase. This is attributed to the circumstance that native soil urease resides in organic colloidal particles with pores large enough for water, urea, ammonia, and carbon dioxide to pass freely, but nevertheless small enough to exclude pronase.

Burns, R. G.↗

Potential Activities and Long Lifetimes of Organic Carbon-Degrading Extracellular Enzymes in Deep Subsurface Sediments of the Baltic Sea

Heterotrophic microorganisms in marine sediments produce extracellular enzymes to hydrolyze organic macromolecules, so their products can be transported inside the cell and used for energy and growth. Therefore, extracellular enzymes may mediate the fate of organic carbon in sediments. The Baltic Sea Basin is a primarily depositional environment with high potential for organic matter preservation. The potential activities of multiple organic carbon-degrading enzymes were measured in samples obtained by the International Ocean Discovery Program Expedition 347 from the Little Belt Strait, Denmark, core M0059C. Potential maximum hydrolysis rates (V max ) were measured at depths down to 77.9mbsf for the following enzymes: alkaline phosphatase, β- d -xylosidase, β- d -cellobiohydrolase, N-acetyl-β- d -glucosaminidase, β-glucosidase, α-glucosidase, leucyl aminopeptidase, arginyl aminopeptidase, prolyl aminopeptidase, gingipain, and clostripain. Extracellular peptidase activities were detectable at depths shallower than 54.95mbsf, and alkaline phosphatase activity was detectable throughout the core, albeit against a relatively high activity in autoclaved sediments. β-glucosidase activities were detected above 30mbsf; however, activities of other glycosyl hydrolases (β-xylosidase, β-cellobiohydrolase, N-acetyl-β-glucosaminidase, and α-glucosidase) were generally indistinguishable from zero at all depths. These extracellular enzymes appear to be extremely stable: Among all enzymes, a median of 51.3% of enzyme activity was retained after autoclaving for an hour. We show that enzyme turnover times scale with the inverse of community metabolic rates, such that enzyme lifetimes in subsurface sediments, in which metabolic rates are very slow, are likely to be extraordinarily long. A back-of-the-envelope calculation suggests enzyme lifetimes are, at minimum, on the order of 230days, and may be substantially longer. These results lend empirical support to the hypothesis that a population of subsurface microbes persist by using extracellular enzymes to slowly metabolize old, highly degraded organic carbon.

54 ENVIRONMENTAL SCIENCES↗

Coupled Hydrological-Thermal-Biogeochemical Modeling for Predicting Arctic Carbon Emissions (CH4PACE)

The Arctic, with nearly 1,700 billion metric tons of carbon stored in its soils, is experiencing significant warming trends that raise concerns about the potential release of greenhouse gases, particularly methane. This report investigates the conversion of carbon stored in Arctic soils and permafrost into methane and its subsequent atmospheric release over the coming decades. Recent data indicate a rise in global methane concentrations, highlighting the importance of understanding the mechanisms of methane generation under anaerobic conditions prevalent in thawing permafrost. Our study employs a multi-faceted approach that integrates fieldwork, benchtop experiments, and numerical simulations to explore the subsurface hydrological-thermal-biogeochemical systems influencing methane emissions. We focus on the relationship between microbial activity in decomposing organic matter under oxygen-limited conditions and the transport of methane out of these saturated wetland soils. Key hydrological parameters, including permeability, porosity, and thermal conductivity, were measured on soil samples from Fairbanks, Alaska, and used to parameterize PFLOTRAN, a coupled hydrological-thermal-reactive transport simulator. Our model enables prediction of the evolution of the active layer and its impact on methane production and release. Our findings underscore the critical need for a mechanistic understanding of methane dynamics in permafrost environments to improve predictions of methane emissions in Earth systems models.

54 ENVIRONMENTAL SCIENCES↗

Status and future of high energy diffuse gamma-ray astronomy

There are two distinctly different high energy diffuse gamma-ray components, one well correlated with broad galactic features and the other apparently isotropic and presumably extragalactic. The observed diffuse galactic high energy gamma radiation is generally thought to be produced in interactions between the cosmic rays and the interstellar matter and photons. It should then ultimately be possible to obtain from the diffuse galactic emission a detailed picture of the galactic cosmic-ray distribution, a high contrast view of the general structure of the galaxy, and further insight into molecular clouds. Two of the candidates for the explanation of the extragalactic diffuse radiation are the sum of emission from active galaxies and matter-antimatter annihilation. A major advancement in the study of the properties of both galactic and extragalactic gamma radiation should occur over the next decade.

Fichtel, C. E.↗

Topological Materials for Functional Optoelectronic Devices

The recent realization of topology as a mathematical concept in condensed matter systems has shattered Landau's widely accepted classification of phases by spontaneous symmetry breaking as he famously said, “a particular symmetry property exists or does not exist.” Topological materials (TMs) such as topological insulators and topological semimetals, are characterized by properties that depend on the topology of the band structure. Such dependence has drastic implications on the optical, electrical, and thermal properties of the material. Fundamental physics of TMs is currently under active research in condensed matter, materials science, and high energy physics. Here, recent advances in exploiting the unique properties of TMs to realize functional optoelectronic devices are surveyed. Current and future applications that are, or may be, enabled by their unique properties are discussed. Although many theoretical ideas have been proposed over the past decade or so on using TMs in optoelectronic applications, the focus will be on experimentally realized devices.

36 MATERIALS SCIENCE↗

Active Fluids Form System-Spanning Filamentary Networks

Recent experimental realizations of liquid-liquid phase separation of active liquid crystals have offered an insight into the interaction between phase separation, ubiquitous in soft matter and biology, and chaotic active flows. Here, in this Letter, we use continuum theory to examine phase separation of an active liquid crystal and a passive fluid and report two new results. First, we provide an analytical derivation of the activity-induced suppression of the phase boundary of the coexistence region—a result first reported in simulations and experiments. We show that the shift in the critical point is a result of the balance between self-stirring active flows and phase-separating diffusive fluxes. Second, we show that this same balance is responsible for dramatically changing the morphology of the phase separated state, resulting in the emergence of a new mixed active phase consisting of a dynamical filamentous active network that invades the entire system area, trapping droplets of passive material. This structure exists even for very low volume fractions of active material. Our work provides an important step towards the goal of understanding how to use activity as a new handle for sculpting interfaces.

active nematics↗

Black hole accretion disks with coronae

Observations suggest the existence of both hot and cold dark matter in the centers of active galactic nuclei. Recent spectral models require a major fraction of power to be dissipated in the hot matter. We study the case when the hot matter forms a corona around a standard cold alpha-disk. In particular, we investigate the case when a major fraction, f, of the power released when the cold matter accretes is transported to and dissipated in the corona. This has major effects on the cold disk, making it colder, more geometrically thin, denser, and having larger optical depths. One important consequence is the disappearance of the effectively optically thin zone as well as of the radiation pressure dominated zone for values of f sufficiently closed to unity. The disappearance of the radiation pressure dominated zone will result in a cold disk with only a gas pressure dominated zone that is stable against thermal and viscous instabilities. We also show that the pressure ( and the radiation) from the corona will only affect the surface layers of the cold disk. Our results disagree with those of other recent work on accretion disks with coronae. We find those works to be based on unphysical assumptions.

Svensson, Roland↗

Large-volume centimeter-wave cavities for axion searches

The scan rate of an axion haloscope is proportional to the square of the cavity volume. In this paper, a new class of thin-shell cavities are proposed to search for axionic dark matter. These cavities feature active volume much larger (>20×) than that of a conventional cylindrical haloscope, comparable quality factor Q, and a similar frequency tuning range. Furthermore, full 3D numerical finite-element analyses have been used to show that the TM 010 eigenmodes are singly polarized throughout the volume of the cavity and can facilitate axion-photon conversion in uniform magnetic field produced by a superconducting solenoid. To mitigate spurious mode crowding and volume losses due to localization, a pre-amplification binary summing network will be used for coupling. Because of the favorable frequency-scaling, the new cavities are most suitable for centimeter-wavelength (~ 10–100 GHz), corresponding to the promising post-inflation axion production window. In this frequency range, the tight machining tolerances required for high-Q thin-shell cavities are achievable with standard machining techniques for near-infrared mirrors.

79 ASTRONOMY AND ASTROPHYSICS↗

Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea

Subsurface oxygen maxima (SOMs) occur directly beneath the mixed layer of stratified water columns across oligotrophic open ocean basins and have been associated with physical transport processes and localized increases in phytoplankton net primary productivity (NPP). We explore the hypothesis that viral lysis (i.e., the ‘viral shunt’) increases nutrient recycling and enhances NPP, supporting SOM formation in stratified water columns, focusing on a recurring SOM at the Bermuda Atlantic Time Series (BATS) in the Sargasso Sea. Reanalysis of historical BATS data showed enhanced Prochlorococcus and virus-like particle abundances associated with SOMs. Instances of high rates of primary and secondary production observed with oxygen supersaturation further implicate a biological mechanism for SOM formation. Leveraging metatranscriptomes, metaviromes, and polony-based data collected during a Lagrangian cruise (October 2019), we link the viral shunt to SOMs, including evidence of elevated cyanophage abundance and infection of Prochlorococcus, and transcriptomic evidence of increased organic matter uptake (i.e., catabolic activity) by copiotrophic bacteria. Cruise data also showed Prochlorococcus nitrogen metabolism transcripts consistent with increased responsiveness to bacterial remineralization. These findings illustrate the biogeochemical impacts of enhanced viral lysis in marine systems, including the potential role of the viral shunt in facilitating SOM formation in the oligotrophic oceans.

Gilbert, Naomi E. [Univ. of Tennessee, Knoxville, ↗

Optically controlled single-valley exciton doublet states with tunable internal spin structures and spin magnetization generation

Manipulating quantum states through light–matter interactions has been actively pursued in two-dimensional materials research. Significant progress has been made toward the optical control of the valley degrees of freedom in semiconducting monolayer transition-metal dichalcogenides, based on doubly degenerate excitons from their two distinct valleys in reciprocal space. Here, we introduce a type of optically controllable doubly degenerate exciton states that come from a single valley, dubbed as single-valley exciton doublet (SVXD) states. They are unique in that their constituent holes originate from the same valence band, making possible the direct optical control of the spin structure of the excited constituent electrons. Combining ab initio GW plus Bethe–Salpeter equation ( GW -BSE) calculations and a theoretical analysis method, we demonstrate such SVXD in substrate-supported monolayer bismuthene—which has been successfully grown using molecular beam epitaxy. In each of the two distinct valleys in the Brillouin zone, strong spin–orbit coupling and C 3 v symmetry lead to a pair of degenerate 1s exciton states (the SVXD states) with opposite spin configurations. Any coherent linear combinations of the SVXD in a single valley can be excited by light with a specific polarization, enabling full manipulation of their internal spin configurations. In particular, a controllable net spin magnetization can be generated through light excitation. Our findings open routes to control quantum degrees of freedom, paving the way for applications in spintronics and quantum information science.

2D materials↗

Cosmological dependence of sterile neutrino dark matter with self-interacting neutrinos

Unexplored interactions of neutrinos could be the key to understanding the nature of the dark matter (DM). In particular, active neutrinos with new self-interactions can produce keV-mass sterile neutrinos that account for the whole of the DM through the Dodelson-Widrow mechanism for a large range of active-sterile mixing values. This production typically occurs before Big-Bang Nucleosynthesis (BBN) in a yet uncharted era of the Universe. We assess how the mixing range for keV-mass sterile neutrino DM is affected by the uncertainty in the early Universe pre-BBN cosmology. This is particularly relevant for identifying the viable parameter space of sterile neutrino searches allowed by all astrophysical limits, as well as for cosmology, since the detection of a sterile neutrino could constitute the first observation of a particle providing information about the pre-BBN epoch. Here, we find that the combined uncertainties in the early Universe cosmology and neutrino interactions significantly expand the allowed parameter space for sterile neutrinos that can constitute the whole of the DM.

79 ASTRONOMY AND ASTROPHYSICS↗

Deep learning of interface structures from simulated 4D STEM data: cation intermixing vs. roughening ∗

Abstract Interface structures in complex oxides remain an active area of condensed matter physics research, largely enabled by recent advances in scanning transmission electron microscopy (STEM). Yet the nature of the STEM contrast in which the structure is projected along the given direction precludes separation of possible structural models. Here, we utilize deep convolutional neural networks (DCNN) trained on simulated 4D STEM datasets to predict structural descriptors of interfaces. We focus on the widely studied interface between LaAlO 3 and SrTiO 3 , using dynamical diffraction theory and leveraging high performance computing to simulate thousands of possible 4D STEM datasets to train the DCNN to learn properties of the underlying structures on which the simulations are based. We test the DCNN on simulated data and show that it is possible (with >95% accuracy) to identify a physically rough from a chemically diffuse interface and create a DCNN regression model to predict step positions. We quantify the applicability of the model to different thicknesses and the transferability of the approach. The method shown here is general and can be applied for any inverse imaging problem where forward models are present.

42 ENGINEERING↗

Estimating ionization states and continuum lowering from ab initio path integral Monte Carlo simulations for warm dense hydrogen

Warm dense matter (WDM) is an active field of research, with applications ranging from astrophysics to inertial confinement fusion. Ionization degree and continuum lowering are important quantities to understand how materials behave under these conditions, but can be difficult to diagnose since experimental campaigns are limited and often require model-dependent analysis. This is especially true for hydrogen, which has a comparably low scattering cross section, making high-quality data particularly difficult to obtain. Consequently, building equation of state tables often relies on simulations in combination with untested approximations to extract properties from experiments. Here, we investigate an approach for extracting the ionization potential depression and ionization degree—quantities which are otherwise not directly accessible from the physical model—from first-principles path integral Monte Carlo (PIMC) simulations utilizing a chemical model. In contrast to experimental measurements, where noise and nonequilibrium effects add to the uncertainty of the inferred parameters, PIMC simulations provide a clean signal with well-defined thermodynamic conditions. Comparisons against commonly used models show a qualitative agreement, but we find deviations primarily for the high-density and high-temperature cases. We also demonstrate the decreasing sensitivity of the dynamic structure factor with respect to both ionization and continuum lowering for increasing scattering angles in x-ray Thomson scattering experiments. Our work has important implications for the design of future experiments, but also offers qualitative understanding of structure factors and the imaginary-time correlation function obtained from first-principles quantum Monte Carlo simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Enzyme activity in terrestrial soil in relation to exploration of the Martian surface

Urease activity in soil is persistent for long periods under low water, low temperature, and sterile regimes, and it was suggested that some form of enzyme-protective mechanism exists in soil. Dublin soil was extracted by sonication in water followed by adding a mixture of salts. Urease activity is associated with the organo-mineral complex thus obtained and is resistant to the activities of proteolytic enzymes. Clay free soil organic matter prepared subsequently by filtration also exhibits urease activity which is resistant to proteolysis. Models consisting of enzymes with bentonite and lignin were found to mimic this resistance to proteolysis. A model system is presented which suggests both the origin and location of soil ureases and a reason for their persistence in nature.

Ardakani, M. S.↗

Nonlinear models for estimating GSFC travel requirements

A methodology is presented for estimating travel requirements for a particular period of time. Travel models were generated using nonlinear regression analysis techniques on a data base of FY-72 and FY-73 information from 79 GSFC projects. Although the subject matter relates to GSFX activities, the type of analysis used and the manner of selecting the relevant variables would be of interest to other NASA centers, government agencies, private corporations and, in general, any organization with a significant travel budget. Models were developed for each of six types of activity: flight projects (in-house and out-of-house), experiments on non-GSFC projects, international projects, ART/SRT, data analysis, advanced studies, tracking and data, and indirects.

Buffalano, C.↗