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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Hot droughts in the Amazon provide a window to a future hypertropical climate

Tropical forests represent the warmest and wettest of Earth’s biomes, but with continued anthropogenic warming, they will be pushed to climate states with no current analogue. Droughts in the tropics are already becoming more intense as they occur at successively higher temperatures. Here, in this study, we synthesize multiple datasets to assess the effects of hot droughts on a central Amazon forest. First, a more than 30-year record of annually resolved forest demographic data from a selective logging experiment showed higher tree mortality during intense droughts, particularly among fast-growing pioneer species with low wood density. Second, analysis of ecophysiological field measurements from the 2015 and 2023 El Niño droughts identified a soil moisture threshold beyond which transpiration rates rapidly declined. As rainless days beyond this threshold continued, drought conditions intensified, increasing the potential for tree mortality from hydraulic failure and carbon starvation. Third, analyses from the Coupled Model Intercomparison Project Phase 6 demonstrated that under high-emission scenarios, a large area of tropical forest will shift to a hotter ‘hypertropical’ climate by 2100. Last, under a hypertropical climate, temperature and moisture conditions during typical dry season months will more frequently exceed identified drought mortality thresholds, elevating the risk of forest dieback. Present-day hot droughts are harbingers of this emerging climate, offering a window for studying tropical forests under expected extreme future conditions.

drought↗
DOE OSTI2016

MicroXRF tomographic visualization of zinc and iron in the zebrafish embryo at the onset of the hatching period

Transition metals such as zinc, copper, and iron play key roles in cellular proliferation, cell differentiation, growth, and development. Over the past decade, advances in synchrotron X-ray fluorescence instrumentation presented new opportunities for the three-dimensional mapping of trace metal distributions within intact specimens. Taking advantage of microXRF tomography, we visualized the 3D distribution of zinc and iron in a zebrafish embryo at the onset of the hatching period. The reconstructed volumetric data revealed distinct differences in the elemental distributions, with zinc predominantly localized to the yolk and yolk extension, and iron to various regions of the brain as well as the myotome extending along the dorsal side of the embryo. The data set complements an earlier tomographic study of an embryo at the pharyngula stage (24 hpf), thus offering new insights into the trace metal distribution at key stages of embryonic development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Low damping (111) oriented lithium aluminum ferrite thin films for spin wave applications

Spin wave-based spintronics are an alternative to conventional electronics due to their potential for efficient energy consumption, improved processing speed, and smaller device dimensions. Low damping magnetic insulators provide the medium for efficient propagation of spin waves for information transfer. Here, we have synthesized by pulsed laser deposition epitaxial spinel structure ferrite thin films of Li 0.5 (Al 1.0 Fe 1.5 )O 4 (LAFO) on (111)-oriented MgAl 2 O 4 that support isotropic magnon propagation in the film plane. Our ferromagnetic resonance measurements show low magnetic damping with a typical Gilbert damping parameter of α = 0.006 and weak-spin–orbit coupling with g = 2.02. These films have low effective magnetization, μ o M eff = 20 mT, similar to that of yttrium iron garnet, the gold standard of low loss magnetic insulators. Our findings show that LAFO is a good candidate as a spin wave medium since it can be grown at low temperatures in different crystal orientations.

Takana, Lerato [Stanford Univ., CA (United States)↗
DOE OSTI2013

Structural basis for Marburg virus VP35-mediated immune evasion mechanisms

Filoviruses, marburgvirus (MARV) and ebolavirus (EBOV), are causative agents of highly lethal hemorrhagic fever in humans. MARV and EBOV share a common genome organization but show important differences in replication complex formation, cell entry, host tropism, transcriptional regulation, and immune evasion. Multifunctional filoviral viral protein (VP) 35 proteins inhibit innate immune responses. Recent studies suggest double-stranded (ds)RNA sequestration is a potential mechanism that allows EBOV VP35 to antagonize retinoic-acid inducible gene-I (RIG-I) like receptors (RLRs) that are activated by viral pathogen–associated molecular patterns (PAMPs), such as double-strandedness and dsRNA blunt ends. Here, we show that MARV VP35 can inhibit IFN production at multiple steps in the signaling pathways downstream of RLRs. The crystal structure of MARV VP35 IID in complex with 18-bp dsRNA reveals that despite the similar protein fold as EBOV VP35 IID, MARV VP35 IID interacts with the dsRNA backbone and not with blunt ends. Functional studies show that MARV VP35 can inhibit dsRNA-dependent RLR activation and interferon (IFN) regulatory factor 3 (IRF3) phosphorylation by IFN kinases TRAF family member-associated NFkb activator (TANK) binding kinase-1 (TBK-1) and IFN kB kinase e (IKKe) in cell-based studies. We also show that MARV VP35 can only inhibit RIG-I and melanoma differentiation associated gene 5 (MDA5) activation by double strandedness of RNA PAMPs (coating backbone) but is unable to inhibit activation of RLRs by dsRNA blunt ends (end capping). In contrast, EBOV VP35 can inhibit activation by both PAMPs. Insights on differential PAMP recognition and inhibition of IFN induction by a similar filoviral VP35 fold, as shown here, reveal the structural and functional plasticity of a highly conserved virulence factor.

Ramanan, Parameshwaran↗
DOE OSTI2022

Liquid Argon Time Projection Chamber Trigger Development with MicroBooNE

The Micro Booster Neutrino Experiment (MicroBooNE) is a Liquid Argon Time Projection Chamber (LArTPC) neutrino detector at Fermilab that has been operating since 2015. It aims to perform v-Ar cross-section measurements, explore the low-energy excess reported by the MiniBooNE experiment and perform a combined search for sterile neutrino oscillations as part of three LArTPCs that make up the Short Baseline Neutrino (SBN) Program at Fermilab. Since MicroBooNE is currently in an R&D phase, it offers a unique opportunity for the implementation and testing of TPC-based triggers as R&D towards the Deep Underground Neutrino Experiment (DUNE). One of the technical challenges of DUNE that we aim to address with this study is that of efficient self-triggering of a LArTPC utilizing TPC signal information. This capability will enable searches for rare processes in DUNE, such as neutrino interactions from a potential galactic supernova burst. This talk will describe the MicroBooNE TPC readout system and ongoing R&D efforts to develop and demonstrate TPC-based triggering.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Dynamic nitrogen fixation in an aerobic endophyte of Populus

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte–poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15 N 2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant–endophyte interactions.

15 N-tracking metabolomics↗
DOE OSTI2024

Exploring Structural Anisotropy in Amorphous Tb-Co via Changes in Medium-Range Ordering

Amorphous thin films grown by magnetron co-sputtering exhibit changes in atomic structure with varying growth and annealing temperatures. Structural variations influence the bulk properties of the films. Scanning nanodiffraction performed in a transmission electron microscope (TEM) is applied to amorphous Tb 17 Co 83 (a-Tb-Co) films deposited over a range of temperatures to measure relative changes in medium-range ordering (MRO). These measurements reveal an increase in MRO with higher growth temperatures and a decrease in MRO with higher annealing temperatures. The trend in MRO indicates a relationship between the growth conditions and local atomic ordering. By tilting select films, the TEM measures variations in the local atomic structure as a function of orientation within the films. The findings support claims that preferential ordering along the growth direction results from temperature-mediated adatom configurations during deposition, and that oriented MRO correlates with increased structural anisotropy, explaining the strong growth-induced perpendicular magnetic anisotropy found in rare earth–transition metal films. Beyond magnetic films, we propose the tilted FEM workflow as a method of extracting anisotropic structural information in a variety of amorphous materials with directionally dependent bulk properties, such as films with inherent bonding asymmetry grown by physical vapor deposition.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis

Abstract WhiB1 is a monomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress in M. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 Å-resolution crystal structure of the [4Fe–4S] cluster-bound (holo-) WhiB1 in complex with the C-terminal domain of the σ70-family primary sigma factor σA of M. tuberculosis containing the conserved region 4 (σA4). Region 4 of the σ70-family primary sigma factors is commonly used by transcription factors for gene activation, and holo-WhiB1 has been proposed to activate gene expression via binding to σA4. The complex structure, however, unexpectedly reveals that the interaction between WhiB1 and σA4 is dominated by hydrophobic residues in the [4Fe–4S] cluster binding pocket, distinct from previously characterized canonical σ704-bound transcription activators. Furthermore, we show that holo-WhiB1 represses transcription by interaction with σA4in vitro and that WhiB1 must interact with σA4 to perform its essential role in supporting cell growth in vivo. Together, these results demonstrate that holo-WhiB1 regulates gene expression by a non-canonical mechanism relative to well-characterized σA4-dependent transcription activators.

Wan, Tao↗
DOE OSTI2022

Soil resistance and recovery during neotropical forest succession

The recovery of soil conditions is crucial for successful ecosystem restoration and, hence, for achieving the goals of the UN Decade on Ecosystem Restoration. Here, we assess how soils resist forest conversion and agricultural land use, and how soils recover during subsequent tropical forest succession on abandoned agricultural fields. Our overarching question is how soil resistance and recovery depend on local conditions such as climate, soil type and land-use history. For 300 plots in 21 sites across the Neotropics, we used a chronosequence approach in which we sampled soils from two depths in old-growth forests, agricultural fields (i.e. crop fields and pastures), and secondary forests that differ in age (1–95 years) since abandonment. We measured six soil properties using a standardized sampling design and laboratory analyses. Soil resistance strongly depended on local conditions. Croplands and sites on high-activity clay (i.e. high fertility) show strong increases in bulk density and decreases in pH, carbon (C) and nitrogen (N) during deforestation and subsequent agricultural use. Resistance is lower in such sites probably because of a sharp decline in fine root biomass in croplands in the upper soil layers, and a decline in litter input from formerly productive old-growth forest (on high-activity clays). Soil recovery also strongly depended on local conditions. During forest succession, high-activity clays and croplands decreased most strongly in bulk density and increased in C and N, possibly because of strongly compacted soils with low C and N after cropland abandonment, and because of rapid vegetation recovery in high-activity clays leading to greater fine root growth and litter input. Furthermore, sites at low precipitation decreased in pH, whereas sites at high precipitation increased in N and decreased in C : N ratio. Extractable phosphorus (P) did not recover during succession, suggesting increased P limitation as forests age. These results indicate that no single solution exists for effective soil restoration and that local site conditions should determine the restoration strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Simulation-Guided Decision-Making for Enhancing Energy Resilience in a Remote Alaskan Community

The increasing frequency and severity of extreme weather events underscore the need to bolster the resilience of energy infrastructure in remote coastal communities exposed to climate hazards. In recent years, considerable effort has been made to harden the grid infrastructure of remote communities through investment in energy storage, advanced metering, renewable generation and energy-efficient loads. However, simulation-based studies are still needed to identify appropriate locations for investment and determine the adequacy of existing infrastructure in supporting new resources. Preparing the required models may often be challenging due to insufficient metering, disparate data sources and workforce limitations. This paper describes modeling efforts undertaken to represent, within a unified co-simulation platform: (a) the electric distribution network and (b) the thermal behavior of a community medical center, in the remote community of Cordova, Alaska. With the help of case-studies, it is shown how the developed simulation platform can help the local utility in making decisions regarding capital investment aimed at enhancing community resilience.

Microgrid, energy storage, resilience↗
DOE OSTI2020

Cybersecurity Attacks in Vehicular Sensors

Today's modern vehicles contain anywhere from sixty to one-hundred sensors and exhibit the characteristics of Cyber-Physical-Systems (CPS). There is a high degree of coupling, cohesiveness, and interactions among vehicle's CPS components (e.g., sensors, devices, systems, systems-of-systems) across sensing, communication, and control layers. Cyber-attacks in the sensing or communication layers can compromise the security of the control layer. This paper provides a detailed review of potential cyber threats related to the sensing layer. Notably, the focus is mainly towards two categories of sensors: vehicle dynamics sensors (e.g., Tire Pressure Monitoring Systems (TPMS), magnetic encoders, and inertial sensors) and environment sensors (e.g., Light Detection and Ranging (LiDAR), ultrasonic, camera, Radio Detection and Ranging (Radar) systems, and Global Positioning System (GPS) units). Furthermore, the paper also offers perspectives through existing countermeasures from literature and stresses the need for data-driven cybersecurity solutions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Stability of tropical forest tree carbon-water relations in a rainfall exclusion treatment through shifts in effective water uptake depth

Increasing severity and frequency of drought is predicted for large portions of the terrestrial biosphere, with major impacts already documented in wet tropical forests. Using a 4-year rainfall exclusion experiment in the Daintree Rainforest in northeast Australia, we examined canopy tree responses to reduced precipitation and soil water availability by quantifying seasonal changes in plant hydraulic and carbon traits for 11 tree species between control and drought treatments. Even with reduced soil volumetric water content in the upper 1 m of soil in the drought treatment, we found no significant difference between treatments for predawn and midday leaf water potential, photosynthesis, stomatal conductance, foliar stable carbon isotope composition, leaf mass per area, turgor loss point, xylem vessel anatomy, or leaf and stem nonstructural carbohydrates. While empirical measurements of aboveground traits revealed homeostatic maintenance of plant water status and traits in response to reduced soil moisture, modeled belowground dynamics revealed that trees in the drought treatment shifted the depth from which water was acquired to deeper soil layers. Finally, these findings reveal that belowground acclimation of tree water uptake depth may buffer tropical rainforests from more severe droughts that may arise in future with climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Endophyte‐induced systemic spatial reprogramming of metabolism in Populus trichocarpa roots under drought

Beneficial, facultative endophytes help plants thrive in challenging environments by altering their host's metabolism, but how these cellular scale metabolic changes propagate to the systems biology scale is unknown. In this work, we employed a high-resolution chemical imaging approach to map metabolic changes at the Populus trichocarpa root-zone and cell-type levels combined with machine learning (ML) models to identify root metabolites and exudates that have predictive power over treatment class. We found that a nine-strain consortium of beneficial endophytes differentially altered the metabolome of droughted root tissues in a manner specific to cell type and root zone, with endophyte abundance showing a clear correlation to individual metabolites. Our study demonstrates that integrating spatial metabolomics with ML can reveal localized metabolic patterns linked to root–microbe interactions and generate novel hypotheses about underlying biological mechanisms.

Drought↗
DOE OSTI2023

Wood‐density has no effect on stomatal control of leaf‐level water use efficiency in an Amazonian forest

Forest disturbances increase the proportion of fast-growing tree species compared to slow-growing ones. To understand their relative capacity for carbon uptake and their vulnerability to climate change, and to represent those differences in Earth system models, it is necessary to characterise the physiological differences in their leaf-level control of water use efficiency and carbon assimilation. We used wood density as a proxy for the fast-slow growth spectrum and tested the assumption that trees with a low wood density (LWD) have a lower water-use efficiency than trees with a high wood density (HWD). We selected 5 LWD tree species and 5 HWD tree species growing in the same location in an Amazonian tropical forest and measured in situ steady-state gas exchange on top-of-canopy leaves with parallel sampling and measurement of leaf mass area and leaf nitrogen content. We found that LWD species invested more nitrogen in photosynthetic capacity than HWD species, had higher photosynthetic rates and higher stomatal conductance. Furthermore, contrary to expectations, we showed that the stomatal control of the balance between transpiration and carbon assimilation was similar in LWD and HWD species and that they had the same dark respiration rates.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

VP24-Karyopherin Alpha Binding Affinities Differ between Ebolavirus Species, Influencing Interferon Inhibition and VP24 Stability

Zaire ebolavirus (EBOV), Bundibugyo ebolavirus (BDBV), and Reston ebolavirus (RESTV) belong to the same genus but exhibit different virulence properties. VP24 protein, a structural protein present in all family members, blocks interferon (IFN) signaling and likely contributes to virulence. Inhibition of IFN signaling by EBOV VP24 (eVP24) involves its interaction with the NPI-1 subfamily of karyopherin alpha (KPNA) nuclear transporters. Here, we evaluated eVP24, BDBV VP24 (bVP24), and RESTV VP24 (rVP24) interactions with three NPI-1 subfamily KPNAs (KPNA1, KPNA5, and KPNA6). Using purified proteins, we demonstrated that each VP24 binds to each of the three NPI-1 KPNAs. bVP24, however, exhibited approximately 10-fold-lower KPNA binding affinity than either eVP24 or rVP24. Cell-based assays also indicate that bVP24 exhibits decreased KPNA interaction, decreased suppression of IFN induced gene expression, and a decreased half-life in transfected cells compared to eVP24 or rVP24. Amino acid sequence alignments between bVP24 and eVP24 also identified residues within and surrounding the previously defined eVP24-KPNA5 binding interface that decrease eVP24-KPNA affinity or bVP24-KPNA affinity. VP24 mutations that lead to reduced KPNA binding affinity also decrease IFN inhibition and shorten VP24 half-lives. Here, these data identify novel functional differences in VP24-KPNA interaction and reveal a novel impact of the VP24-KPNA interaction on VP24 stability. The interaction of Ebola virus (EBOV) VP24 protein with host karyopherin alpha (KPNA) proteins blocks type I interferon (IFN) signaling, which is a central component of the host innate immune response to viral infection. Here, we quantitatively compared the interactions of VP24 proteins from EBOV and two members of the Ebolavirus genus, Bundibugyo virus (BDBV) and Reston virus (RESTV). The data reveal lower binding affinity of the BDBV VP24 (bVP24) for KPNAs and demonstrate that the interaction with KPNA modulates inhibition of IFN signaling and VP24 stability. The effect of KPNA interaction on VP24 stability is a novel functional consequence of this virus-host interaction, and the differences identified between viral species may contribute to differences in pathogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2010

Mutations Abrogating VP35 Interaction with Double-Stranded RNA Render Ebola Virus Avirulent in Guinea Pigs

Ebola virus (EBOV) protein VP35 is a double-stranded RNA (dsRNA) binding inhibitor of host interferon (IFN)-{alpha}/{beta} responses that also functions as a viral polymerase cofactor. Recent structural studies identified key features, including a central basic patch, required for VP35 dsRNA binding activity. To address the functional significance of these VP35 structural features for EBOV replication and pathogenesis, two point mutations, K319A/R322A, that abrogate VP35 dsRNA binding activity and severely impair its suppression of IFN-{alpha}/{beta} production were identified. Solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography reveal minimal structural perturbations in the K319A/R322A VP35 double mutant and suggest that loss of basic charge leads to altered function. Recombinant EBOVs encoding the mutant VP35 exhibit, relative to wild-type VP35 viruses, minimal growth attenuation in IFN-defective Vero cells but severe impairment in IFN-competent cells. In guinea pigs, the VP35 mutant virus revealed a complete loss of virulence. Strikingly, the VP35 mutant virus effectively immunized animals against subsequent wild-type EBOV challenge. These in vivo studies, using recombinant EBOV viruses, combined with the accompanying biochemical and structural analyses directly correlate VP35 dsRNA binding and IFN inhibition functions with viral pathogenesis. Moreover, these studies provide a framework for the development of antivirals targeting this critical EBOV virulence factor.

59 BASIC BIOLOGICAL SCIENCES↗