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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

A characterization of recombinant Arabidopsis FRIABLE1 (FRB1) reveals robust rhamnogalacturonan-I rhamnosyltransferase activity and critical catalytic residues

Plant cell walls are glycan-rich extracellular matrices that fundamentally impact essential cellular processes, such as growth, adhesion, and cell shape acquisition. Understanding plant cell wall glycans requires the identification and characterization of the biosynthetic enzymes that produce these polymers. Most successful in vitro protein expression studies of plant cell wall glycosyltransferases have relied on insect, fungal/yeast, or human cell expression systems, whereas prokaryotic expression systems have been generally unsuccessful. Here, we show that Arabidopsis FRIABLE1 (FRB1)/rhamnogalacturonan-I rhamnosyltransferase 8 (RRT8) can be produced in Escherichia coli RosettaGami2 cells as N-terminal maltose-binding protein fusion proteins containing C-terminal 6X-His-tags. We also report the catalytic constants of FRB1/RRT8 with apparent K M and K cat values of 226 μM and 33 min -1 for UDP-Rhamnose and 117 μM and 28.7 min -1 for rhamnogalacturonan-I (RG-I), respectively. We examine the catalytic activities of mutated FRB1/RRT8 proteins based on an AlphaFold 3-generated FRB1/RRT8 protein structural model with a virtually docked UDP-Rha donor. Enzymatic characterization of the mutated and wildtype FRB1/RRT8 protein confirmed that mutation of predicted catalytic site amino acid residues resulted in a 20-fold reduction in RRT activity. FRB1 also robustly polymerizes RG-I in combination with RG-I galacturonosyltransferase 1. These results show how a robust E. coli expression system combined with artificial intelligence tools can be used to increase understanding of plant cell wall glycosyltransferase structure and function.

glycosyltransferase↗
DOE OSTI2022

Choices in land representation materially affect modeled biofuel carbon intensity estimates

Estimates of biofuel carbon intensity are uncertain and depend on modeled land use change (LUC) emissions. While analysts have focused on economic and agronomic assumptions affecting the quantity of land converted, researchers have paid less attention to how models classify land into broad categories and designate some categories as ineligible for LUC. To explore the effect of these land representation attributes, we use three versions of a global human and Earth systems model, GCAM, and compute the “carbon intensity of land-use change” (CI-LUC) from increased U.S. corn ethanol production. We consider uncertainty in model parameters along with the choice of land representation and find the latter is one of the most influential parameters on estimated CI-LUC. A version of the model that protects 90% of non-commercial land reduced estimated CI-LUC by an average of 32% across Monte Carlo trials compared to our baseline model. Another version that mimics the GTAP-BIO-ADV land representation, which protects all non-commercial land, reduced CI-LUC by an average of 19%. The results of this experiment suggest that analyses of LUC that exclude non-commercial land categories or assume more land is protected than empirically justified underestimate biofuel induced LUC GHG emissions.

09 BIOMASS FUELS↗
DOE OSTI2021

CTPS and IMPDH form cytoophidia in developmental thymocytes

The cytoophidium, a filamentous structure formed by metabolic enzymes, has emerged as a novel regulatory machinery for certain proteins. The rate-limiting enzymes of de novo CTP and GTP synthesis, cytidine triphosphate synthase (CTPS) and inosine monophosphate dehydrogenase (IMPDH), are the most characterized cytoophidium-forming enzymes in mammalian models. Although the assembly of CTPS cytoophidia has been demonstrated in various organisms including multiple human cancers, a systemic survey for the presence of CTPS cytoophidia in mammalian tissues in normal physiological conditions has not yet been reported. Herein, we examine major organs of adult mouse and observe that CTPS cytoophidia are displayed by a specific thymocyte population ranging between DN3 to early DP stages. Most of these cytoophidium-presenting cells have both CTPS and IMPDH cytoophidia and undergo rapid cell proliferation. In addition, we show that cytoophidium formation is associated with active glycolytic metabolism as the cytoophidium-presenting cells exhibit higher levels of c-Myc, phospho-Akt and PFK. Inhibition of glycolysis with 2DG, however, disrupts most of cytoophidium structures and impairs cell proliferation. Our findings not only indicate that the regulation of CTPS and IMPDH cytoophidia are correlated with the metabolic switch triggered by pre-TCR signaling, but also suggest physiological roles of the cytoophidium in thymocyte development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment

There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity in a cell-type-specific manner to better understand and predict the function of complex biological systems such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverage due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (microdroplet processing in one pot for trace samples), multiplexed isobaric labeling, and a nanoflow peptide fractionation approach. The integrated workflow allowed us to maximize proteome coverage of laser-isolated tissue samples containing nanogram levels of proteins. We demonstrated that the deep spatial proteomics platform can quantify more than 5000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 μm2) and differentiate unique protein abundance patterns in pancreas. Furthermore, the use of the microPOTS chip eliminated the requirement for advanced microfabrication capabilities and specialized nanoliter liquid handling equipment, making it more accessible to proteomic laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The Climatic Impact‐Driver Framework for Assessment of Risk‐Relevant Climate Information

Abstract The climate science and applications communities need a broad and demand‐driven concept to assess physical climate conditions that are relevant for impacts on human and natural systems. Here, we augment the description of the “climatic impact‐driver” (CID) approach adopted in the Working Group I (WGI) contribution to the Intergovernmental Panel on Climate Change (IPCC) Sixth Assessment Report. CIDs are broadly defined as “physical climate system conditions (e.g., means, events, and extremes) that affect an element of society or ecosystems. Depending on system tolerance, CIDs and their changes can be detrimental, beneficial, neutral, or a mixture of each across interacting system elements and regions.” We give background information on the IPCC Report process that led to the development of the 7 CID types (heat and cold, wet and dry, wind, snow and ice, coastal, open ocean, and other) and 33 distinct CID categories, each of which may be evaluated using a variety of CID indices. This inventory of CIDs was co‐developed with WGII to provide a useful collaboration point between physical climate scientists and impacts/risk experts to assess the specific climatic phenomena driving sectoral responses and identify relevant CID indices within each sector. The CID Framework ensures that a comprehensive set of climatic conditions informs adaptation planning and risk management and may also help prioritize improvements in modeling sectoral dynamics that depend on climatic conditions. CIDs contribute to climate services by increasing coherence and neutrality when identifying and communicating relevant findings from physical climate research to risk assessment and planning activities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Comment on “Five Decades of Observed Daily Precipitation Reveal Longer and More Variable Drought Events Across Much of the Western United States”

Abstract Changes in precipitation patterns with climate change could have important impacts on human and natural systems. Zhang et al. (2021, https://doi.org/10.1029/2020gl092293 ) report trends in daily precipitation patterns over the last five decades in the western United States, focusing on meteorological drought. They report that dry intervals (calculated at the annual or seasonal level) have increased across much of the southwestern U.S., with statistical assessment suggesting the results are statistically robust. However, Zhang et al. (2021, https://doi.org/10.1029/2020gl092293 ) preprocess their annual (or seasonal) averages to compute 5‐year moving window averages before using established statistical techniques for trend analysis that assume independence about some fixed trend. Here we show that the moving window preprocessing violates that independence assumption and inflates the statistical significance of their trend estimates. This raises questions about the robustness of their results. We conclude by discussing the difficulty of adjusting for spatial structure when assessing time trends in a regional context.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Human influence on joint changes in temperature, rainfall and continental aridity

Despite the pervasive impact of drought on human and natural systems, the large-scale mechanisms conducive to regional drying remain poorly understood. Here we use a multivariate approach to identify two distinct externally forced fingerprints from multiple ensembles of Earth system model simulations. The leading fingerprint, F M1 (x), is characterized by global warming, intensified wet–dry patterns and progressive large-scale continental aridification, largely driven by multidecadal increases in greenhouse gas (GHG) emissions. The second fingerprint, F M2 (x), captures a pronounced interhemispheric temperature contrast, associated meridional shifts in the intertropical convergence zone and correlated anomalies in precipitation and aridity over California, the Sahel and India. F M2 (x) exhibits nonlinear temporal behaviour: the intertropical convergence zone moves southwards before 1975 in response to increases in hemispherically asymmetric sulfate aerosol emissions, and it shifts northwards after 1975 due to reduced sulfur dioxide emissions and the GHG-induced warming of Northern Hemisphere landmasses. Both fingerprints are statistically identifiable in observations of joint changes in temperature, rainfall and aridity during 1950–2014. Furthermore, we show that the reliable simulation of these changes requires combined forcing by GHGs, direct and indirect effects of aerosols, and large volcanic eruptions. Our results suggest that GHG-induced aridification may be modulated regionally by future reductions in sulfate aerosol emissions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Precipitation trends determine future occurrences of compound hot–dry events

Compound hot–dry events—co-occurring hot and dry extremes—frequently cause damages to human and natural systems, often exceeding separate impacts from heatwaves and droughts. Strong increases in the occurrence of these events are projected with warming, but associated uncertainties remain large and poorly understood. Here, using climate model large ensembles, we show that mean precipitation trends exclusively modulate the future occurrence of compound hot–dry events over land. This occurs because local warming will be large enough that future droughts will always coincide with at least moderately hot extremes, even in a 2°C warmer world. By contrast, precipitation trends are often weak and equivocal in sign, depending on the model, region and internal climate variability. Therefore, constraining regional precipitation trends will also constrain future compound hot–dry events. These results help to assess future frequencies of other compound extremes characterized by strongly different trends in the drivers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Brominated lipid probes expose structural asymmetries in constricted membranes

Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Global monthly sectoral water use for 2010–2100 at 0.5° resolution across alternative futures

Water usage is closely linked with societal goals that are both local and global in scale, such as sustainable development and economic growth. It is therefore of value, particularly for long-term planning, to understand how future sectoral water usage could evolve on a global scale at fine resolution. Additionally, future water usage could be strongly shaped by global forces, such as socioeconomic and climate change, and the multi-sector dynamic interactions those forces create. We generate a novel global gridded monthly sectoral water withdrawal and consumption dataset at 0.5° resolution for 2010–2100 for a diverse range of 75 scenarios. The scenarios are harmonized with the five Shared Socioeconomic Pathways (SSPs) and four Representative Concentration Pathways (RCPs) scenarios to support its usage in studies evaluating the implications of uncertain human and earth system change for future global and regional dynamics. To generate the data, we couple the Global Change Analysis Model (GCAM) with a land use spatial downscaling model (Demeter), a global hydrologic framework (Xanthos), and a water withdrawal downscaling model (Tethys).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Collaborative energy and land use planning

Energy models make projections for infrastructure, yet struggle to map deployment pathways at the ground level, where risks and benefits to human and natural systems materialize. Furthermore, a study now shows how blending in geospatial science can help to preserve natural capital while allowing for new infrastructure to be built.

Energy and society↗
DOE OSTI2023

Implicit learning of convective organization explains precipitation stochasticity

Accurate prediction of precipitation intensity is crucial for both human and natural systems, especially in a warming climate more prone to extreme precipitation. Yet, climate models fail to accurately predict precipitation intensity, particularly extremes. One missing piece of information in traditional climate model parameterizations is subgrid-scale cloud structure and organization, which affects precipitation intensity and stochasticity at coarse resolution. Here, using global storm-resolving simulations and machine learning, we show that, by implicitly learning subgrid organization, we can accurately predict precipitation variability and stochasticity with a low-dimensional set of latent variables. Using a neural network to parameterize coarse-grained precipitation, we find that the overall behavior of precipitation is reasonably predictable using large-scale quantities only; however, the neural network cannot predict the variability of precipitation (R 2 ~ 0.45) and underestimates precipitation extremes. The performance is significantly improved when the network is informed by our organization metric, correctly predicting precipitation extremes and spatial variability (R 2 ~ 0.9). The organization metric is implicitly learned by training the algorithm on a high-resolution precipitable water field, encoding the degree of subgrid organization. The organization metric shows large hysteresis, emphasizing the role of memory created by subgrid-scale structures. We demonstrate that this organization metric can be predicted as a simple memory process from information available at the previous time steps. These findings stress the role of organization and memory in accurate prediction of precipitation intensity and extremes and the necessity of parameterizing subgrid-scale convective organization in climate models to better project future changes of water cycle and extremes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Safety Benefits Assessment for Accident Tolerant Fuels in Consideration of Steam Generator Tube Degradation Using Dynamic Event Tree Analysis

Accident tolerant fuel (ATF) is expected to delay or prevent core damage by providing additional coping time under accidents involving loss of core cooling. The effect of extended coping time may vary depending on the plant response to accidents. Age-related component degradation that deteriorates plant performance over time could have an impact on the actual advantages of ATF. The potential safety benefits of two near-term ATF candidates, including Cr-coated Zr cladding and FeCrAl cladding, are assessed for a 2-in. loss-of-coolant accident with failed high-pressure safety injection using the dynamic event tree (DET) approach considering possible stress corrosion cracking of steam generator (SG) tubing under aging. The DET approach allows likelihood quantification of accident sequences leading to core damage, including stochastic variation of system response and human actions during accident mitigation. The safety benefits of the selected ATF claddings in terms of additional coping time and the core damage frequency reduction rate under specified accident situations were quantitatively estimated. The results show that the deployment of the two selected ATF claddings is expected to lead to longer coping times and lower core damage frequency due to the wider safety margin to peak cladding temperature they provide. The safety advantages would be greater as SG tube degradation proceeds. Thus, the two ATF candidates would lead to less severe consequences in terms of likelihood of core damage and susceptibility to the SG tube degradation than UO 2 -Zr fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Alignment among environmental programs in higher education: What Food-Energy-Water Nexus concepts are covered in introductory courses?

Interdisciplinary environmental and sustainability (IES) programs are different from other fields because they focus on a complex integration of humanities, social, and natural sciences concepts centered on the interactions of coupled human and natural systems. The interdisciplinary nature of IES programs does not lend itself to traditional discipline-specific concept inventory frameworks for critically evaluating preconceptions and learning. We discuss the results of the first phase of a research project to develop a next generation concept inventory for evaluating interdisciplinary concepts important for introductory IES courses. Using the Food-Energy-Water (FEW) Nexus (the intersections/interdependencies of food, energy, and water sectors) as our focus, we conducted a content analysis of eight representative college-level introductory environmental course syllabi and course materials (e.g., textbooks, journal articles, print media) to identify common interdisciplinary FEW Nexus concepts taught in introductory IES courses. Results demonstrate that all IES introductory course materials reference the FEW Nexus. Food, energy, and/or water resources as individual elements of the FEW Nexus are frequently described, but connections between these resource systems are included less often. Biology, energy systems, waste and pollution in the natural environment, agriculture, earth sciences and geology, climate change, behavioral social sciences, and economics concepts are most associated with FEW concepts, hinting at commonalities across IES topics that anchor systems thinking. Despite differences in IES programs, there appears to be some alignment between core concepts being taught at the FEW Nexus in introductory courses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Historical evaluation and future projections of compound heatwave and drought extremes over the conterminous United States in CMIP6 *

Abstract Independently, both droughts and heatwaves can induce severe impacts on human and natural systems. However, when these two climate extremes occur concurrently in a given region, their compound impacts are often more pronounced. With the improvement in both the spatiotemporal resolution and representation of complex climate processes in the global climate models (GCMs), they are increasingly used to study future changes in these extremes and associated regional impacts. However, GCM selection for such impact assessments is generally based on historical performance and/or future mean changes, without considering individual or compound extremes. In contrast, this study evaluates historical performance and projected changes in heatwaves, droughts, and compound heatwave-droughts using an ensemble of GCMs from the latest Phase 6 of Coupled Models Intercomparison Project at a regional scale across the conterminous United States. Additionally, we explore the inter-model differences in the projected changes that are associated with various characteristics of extremes and the choice of drought indices. Our analysis reveals considerable variation among the GCMs, as well as substantial differences in the projected changes based on the choice of drought indices and region of interest. For example, the projected increases in both the frequency and intensity of drought and associated compound extreme days, based on the standardized precipitation evapotranspiration index far exceed those derived from the standard precipitation index. Further, the largest changes in the frequency of compound extremes are projected over the Southwest, South Central, and parts of the Southeast while the smallest changes are projected over the Northeast. Overall, this study provides important insights for the interpretation and selection of GCMs for future assessment studies that are crucial for the development of regional adaptation strategies in the face of climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Uncovering interpretable relationships in high-dimensional scientific data through function preserving projections

Abstract In many fields of science and engineering, we frequently encounter experiments or simulations datasets that describe the behavior of complex systems and uncovering human interpretable patterns between their inputs and outputs via exploratory data analysis is essential for building intuition and facilitating discovery. Often, we resort to 2D embeddings for examining these high-dimensional relationships (e.g. dimensionality reduction). However, most existing embedding methods treat the dimensions as coordinates for samples in a high-dimensional space, which fail to capture the potential functional relationships, and the few methods that do take function into consideration either only focus on linear patterns or produce non-linear embeddings that are hard to interpret. To address these challenges, we proposed function preserving projections (FPP), which construct 2D linear embeddings optimized to reveal interpretable yet potentially non-linear patterns between the domain and the range of a high-dimensional function. The intuition here is that humans are good at understanding potentially non-linear patterns in 2D but unable to interpret non-linear mapping from high-dimensional space to 2D. Therefore, we should restrict the projection to linear but not the pattern we are seeking. Using FPP on real-world datasets, one can obtain fundamentally new insights about high-dimensional relationships in extremely large datasets that could not be processed with existing dimension reduction methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected

ABSTRACT During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host‐associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.

Environmental Sciences & Ecology↗
DOE OSTI2022

Neuromorphic Computing is Turing-Complete

Neuromorphic computing is a non-von Neumann computing paradigm that performs computation by emulating the human brain. Neuromorphic systems are extremely energy-efficient and known to consume thousands of times less power than CPUs and GPUs. They have the potential to drive critical use cases such as autonomous vehicles, edge computing and internet of things in the future. For this reason, they are sought to be an indispensable part of the future computing landscape. Neuromorphic systems are mainly used for spike-based machine learning applications, although there are some non-machine learning applications in graph theory, differential equations, and spike-based simulations. These applications suggest that neuromorphic computing might be capable of general-purpose computing. However, general-purpose computability of neuromorphic computing has not been established yet. In this work, we prove that neuromorphic computing is Turing-complete and therefore capable of general-purpose computing. Specifically, we present a model of neuromorphic computing, with just two neuron parameters (threshold and leak), and two synaptic parameters (weight and delay). We devise neuromorphic circuits for computing all the μ-recursive functions (i.e., constant, successor and projection functions) and all the μ-recursive operators (i.e., composition, primitive recursion and minimization operators). Given that the μ-recursive functions and operators are precisely the ones that can be computed using a Turing machine, this work establishes the Turing-completeness of neuromorphic computing.

Date, Prasanna↗