A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2
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Spermidine/spermine N-acetyltransferases (SSATs) and other types of polyamine acetyltransferases (PAATs) acetylate diamines and/or polyamines. These enzymes are evolutionarily related and belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily, yet we lack a fundamental understanding of their substrate specificity and/or promiscuity toward different compounds. Many of these enzymes are known or are predicted to acetylate polyamines, but in the cell there are other types of compounds that contain moieties derived from polyamines that may be the native substrates for these enzymes. To learn more about the identity of substrates that are acetylated, we selected and screened 17 different GNAT enzymes for activity toward a set of structurally diverse compounds that contained different types of amine moieties (e.g., aminopropyl, aminobutyl, etc.). These compounds included diamines, triamines, and polyamines containing primary amino groups, and they had structural diversity with variation of the chain length and presence or absence of internal amino groups and other functional groups. We found 12 of the 17 enzymes acetylated at least one of the compounds. Some enzymes were selective toward acetylating only one compound while others exhibited substrate promiscuity toward numerous compounds. Our experimental results ultimately allowed us to pinpoint specific substrates that could be further investigated to more fully understand substrate specificity versus promiscuity of GNAT enzymes and the role of acetylated small molecules in cells.
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Atomically dispersed supported metal catalysts offer new properties and the benefits of maximized metal accessibility and utilization. The characterization of these materials, however, remains challenging. Using atomically dispersed platinum supported on crystalline MgO (chosen for its well-defined bonding sites) as a prototypical example, we demonstrate in this work how systematic density functional theory calculations for assessing all the potentially stable platinum sites, combined with automated analysis of extended X-ray absorption fine structure (EXAFS) spectra, leads to unbiased identification of isolated, surface-enveloped platinum cations as the catalytic species for CO oxidation. The catalyst has been characterized by atomic-resolution imaging and EXAFS and high-energy resolution fluorescence detection X-ray absorption near edge spectroscopy. The proposed platinum sites are in agreement with experiment. This theory-guided workflow leads to rigorously determined structural models and provides a more detailed picture of the structure of the catalytically active site than what is currently possible with conventional EXAFS analyses. As this approach is efficient and agnostic to the metal, support, and catalytic reaction, we posit that it will be of broad interest to the materials characterization and catalysis communities.
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Abstract Understanding the complex interrelationships between wildfire and its environmental and anthropogenic controls is crucial for wildfire modeling and management. Although machine learning (ML) models have yielded significant improvements in wildfire predictions, their limited interpretability has been an obstacle for their use in advancing understanding of wildfires. This study builds an ML model incorporating predictors of local meteorology, land‐surface characteristics, and socioeconomic variables to predict monthly burned area at grid cells of 0.25° × 0.25° resolution over the contiguous United States. Besides these predictors, we construct and include predictors representing the large‐scale circulation patterns conducive to wildfires, which largely improves the temporal correlations in several regions by 14%–44%. The Shapley additive explanation is introduced to quantify the contributions of the predictors to burned area. Results show a key role of longitude and latitude in delineating fire regimes with different temporal patterns of burned area. The model captures the physical relationship between burned area and vapor pressure deficit, relative humidity (RH), and energy release component (ERC), in agreement with the prior findings. Aggregating the contribution of predictor variables of all the grids by region, analyses show that ERC is the major contributor accounting for 14%–27% to large burned areas in the western US. In contrast, there is no leading factor contributing to large burned areas in the eastern US, although large‐scale circulation patterns featuring less active upper‐level ridge‐trough and low RH two months earlier in winter contribute relatively more to large burned areas in spring in the southeastern US.
Because of internal variability in both the real-world and global climate models, it is unclear whether disagreement between models and observations reflects true systematic differences, or different phasing of internal variability in the short observational period. Here, we address this issue through an examination of moderate-to-heavy precipitation in large ensembles of global climate models. We find that model inconsistency with a global observational product is lowest for extratropical precipitation in northern hemisphere winter. The inconsistency is systematically greater for the southern hemisphere winter, but the difference between hemispheres could be due to observational quality. Moderate-to-heavy extratropical winter precipitation is less inconsistent than moderate-to-heavy tropical precipitation in most models. Within the tropics, moderate-to-heavy precipitation is particularly inconsistent with the reference in regions including the Caribbean (especially during JJA), the northern and southern flanks of the Pacific and Atlantic ITCZ, and the Indian Ocean.
The export of dissolved organic carbon (DOC) from a watershed is a key component of the terrestrial biosphere carbon cycle. There is a need to improve our understanding of how and by how much various environmental factors are driving the temporal patterns of DOC export in order to accurately model and evaluate terrestrial carbon storage and fluxes. In this synthesis, we compiled observational data sets from 14 watersheds in the conterminous United States spanning the time period from 1981 to 2017. We used these data sets to examine the relative impacts of various climate, atmospheric deposition, and land cover factors on the temporal patterns of DOC export across watersheds of different sizes and landscape conditions, as well as the time-series autocorrelation of DOC export. Overall, our results suggest that the dominant factor on an annual scale was the amount of precipitation, which had a positive correlation with DOC export from a watershed. Overall increasing nitrogen deposition was coincident with increasing DOC export, and increasing sulfur deposition was coincident with declining DOC export. The seasonal pattern of DOC export was strongly regulated by air temperature, the long-term trend was negatively influenced by increasing sulfur deposition, and no obvious autocorrelation was detected in DOC export. In addition, higher rates of DOC export were positively correlated with greater area of wetlands within a watershed, but was not found to be strongly related to any of the other land cover types.
As marginalized communities continue to bear disproportionate impacts from environmental hazards, we urgently call for researchers and institutions to elevate the principles of Environmental Justice. The American Geophysical Union (AGU) GeoHealth section supports members' engagement in health-related community-engaged and community-led transdisciplinary research. We highlight intersectional research that provides examples and actions for both individuals and organizations on community science and trust building, removing barriers created by scientific agency priorities and career expectations, and opportunities in education and policy. Justice does not start or end at one meeting; this is ongoing work that is active, evolving, and an ethical responsibility of AGU's membership.
Thin current sheets (TCSs) have been postulated to be a necessary precondition for reconnection onset. Magnetic reconnection X-lines in the magnetotail have been observed to be more common duskward of midnight. We take advantage of the MMS tetrahedral formation during the 2017–2020 MMS tail seasons to calculate the thickness of the cross-tail neutral sheet relative to ion gyroradius. While a similar technique was applied to Cluster data, current sheet thickness over a broader range of radial distances has not been robustly explored before this study. We compare our analysis to recent theories regarding mechanisms of tail current sheet thinning and to recent simulations. We find MMS spent more than twice as long in ion-scale TCSs in the pre-midnight sector than post-midnight, despite nearly even plasma sheet dwell time. The dawn-dusk asymmetry in the distribution of Ion Diffusion Regions, as previously reported in relation to regions of TCSs, is also analyzed.
Hyperspectral remote sensing has the potential to map numerous attributes of the Earth’s surface, including spatial patterns of biological diversity. Grasslands are one of the largest biomes on Earth. Accurate mapping of grassland biodiversity relies on spectral discrimination of endmembers of species or plant functional types. We focused on spectral separation of grass lineages that dominate global grassy biomes: Andropogoneae (C 4 ), Chloridoideae (C 4 ), and Pooideae (C 3 ). We examined leaf reflectance spectra (350–2,500 nm) from 43 grass species representing these grass lineages from four representative grassland sites in the Great Plains region of North America. Here, we assessed the utility of leaf reflectance data for classification of grass species into three major lineages and by collection site. Classifications had very high accuracy (94%) that were robust to site differences in species and environment. We also show an information loss using multispectral sensors, that is, classification accuracy of grass lineages using spectral bands provided by current multispectral satellites is much lower (accuracy of 85.2% and 61.3% using Sentinel 2 and Landsat 8 bands, respectively). Our results suggest that hyperspectral data have an exciting potential for mapping grass functional types as informed by phylogeny. Leaf-level hyperspectral separability of grass lineages is consistent with the potential increase in biodiversity and functional information content from the next generation of satellite-based spectrometers.
Abstract Magnetic reconnection often initiates abruptly and then rapidly progresses to a nonlinear quasi‐steady state. While satellites frequently detect reconnection events, ascertaining whether the system has achieved steady‐state or is still evolving in time remains challenging. Here, we propose that the relatively rapid opening of the reconnection separatrices within the electron diffusion region serves as an indicator of the growth phase of reconnection. The opening of the separatrices is produced by electron flows diverging away from the neutral line downstream of the X‐line and flowing around a dipolarization front. This flow pattern leads to characteristic spatial structures in the electron pressure‐strain interaction that could be a useful indicator for the growth phase of a reconnection event. We employ two‐dimensional particle‐in‐cell numerical simulations of anti‐parallel magnetic reconnection to validate this prediction. We find that the signature discussed here, alongside traditional reconnection indicators, can serve as a marker of the growth phase. This signature is potentially accessible using multi‐spacecraft single‐point measurements, such as with NASA's Magnetospheric Multiscale satellites in Earth's magnetotail. Applications to other settings where reconnection occurs are also discussed.