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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Influence of Microbial Priming Effects on the Hydro-bio-geochemistry of Large River Reservoirs

River-tributary confluences, where diverse organic matter (OM) sources mix, are considered aquatic critical zones for biogeochemical cycling. Here we evaluate dissolved OM composition and bioavailability in the mainstem of the Columbia River and three of its tributaries (Snake, Yakima, and Walla Walla rivers) along a hydrologic gradient in the Columbia River drainage basin using a variety of bulk and molecular level measurements. Field replicates and mixtures representing river-tributary confluences were incubated in the dark for 15 days to investigate the response of the microbial community to varying OM quantity/composition. The Columbia, Snake, and Yakima rivers did not differ in dissolved organic carbon (DOC), fluorescent dissolved OM (fDOM), or Chlorophyll-a (Chl-a) concentrations. However, the Walla Walla River had significantly greater DOC, fDOM, and Chl-a concentrations, indicative of greater contributions from algal DOM. FT-ICR-MS spectra for Walla Walla had significantly more peaks corresponding to amino sugars, carbohydrates and proteins while the Columbia River had more peaks for lignin, unsaturated hydrocarbons, and condensed aromatics. When incubated for 15 days in the dark, total DOC did not decrease for any of the river samples. DOC did decrease, however, in a mix representing the confluence of the Columbia and Walla Walla rivers, suggesting the microbial consortia of the Columbia River were primed by the Walla Walla River OM. OM composition was significantly different for several compound classes (e.g., lignin, protein, and tannin) following the incubations of unmixed river and tributary samples. However, the microbial community in the Walla Walla-Columbia mixture appeared to be indiscriminate of the molecular structure of the DOM as the compound class distribution did not change significantly. This provides preliminary evidence that the heterotrophs in river-tributary critical zones remineralize diverse OM structures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Measurement of CP asymmetries in ${D}_{(s)}^{+}\to \eta {\pi}^{+}$ and ${D}_{(s)}^{+}\to {\eta}^{\prime }{\pi}^{+}$ decays

Searches for CP violation in the decays ${D}_{(s)}^{+}\to \eta {\pi}^{+}$ and ${D}_{(s)}^{+}\to {\eta}^{\prime }{\pi}^{+}$ are performed using pp collision data corresponding to 6 fb –1 of integrated luminosity collected by the LHCb experiment. The calibration channels ${D}_{(s)}^{+}\to \phi {\pi}^{+}$ are used to remove production and detection asymmetries. The resulting CP-violating asymmetries are $\mathcal{A}^{CP} = (D^+ \to ηπ^+) = (0.34 ± 0.66 ± 0.16 ± 0.05)$ %, $\mathcal{A}^{CP} = (D^+_s \to ηπ^+) = (0.32 ± 0.51 ± 0.12)$ %, $\mathcal{A}^{CP} = (D^+ \to η'π^+) = (0.49 ± 0.18 ± 0.06 ± 0.05)$ %, $\mathcal{A}^{CP} = (D^+_s \to η'π^+) = (0.01 ± 0.12 ± 0.08)$ %, where the first uncertainty is statistical, the second is systematic and the third, relevant for the D + channels, is due to the uncertainty on ${\mathcal{A}}^{CP}=\left({D}^{+}\to \phi {\pi}^{+}\right)$. These measurements, currently the most precise for three of the four channels considered, are consistent with the absence of CP violation. A combination of these results with previous LHCb measurements is presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Vegetation Type and Decomposition Priming Mediate Brackish Marsh Carbon Accumulation Under Interacting Facets of Global Change

Coastal wetland carbon pools are globally important, but their response to interacting facets of global change remain unclear. Numerical models neglect species-specific vegetation responses to sea level rise (SLR) and elevated CO 2 (eCO 2 ) that are observed in field experiments, while field experiments cannot address the long-term feedbacks between flooding and soil growth that models show are important. Here, we present a novel numerical model of marsh carbon accumulation parameterized with empirical observations from a long-running eCO 2 experiment in an organic rich, brackish marsh. Model results indicate that eCO 2 and SLR interact synergistically to increase soil carbon burial, driven by shifts in plant community composition and soil volume expansion. Furthermore, newly parameterized interactions between plant biomass and decomposition (i.e. soil priming) reduce the impact of eCO 2 on marsh survival, and by inference, the impact of eCO 2 on soil carbon accumulation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Priming self-assembly pathways by stacking block copolymers

Abstract Block copolymers spontaneously self-assemble into well-defined nanoscale morphologies. Yet equilibrium assembly gives rise to a limited set of structures. Non-equilibrium strategies can, in principle, expand diversity by exploiting self-assembly’s responsive nature. In this vein, we developed a pathway priming strategy combining control of thin film initial configurations and ordering history. We sequentially coat distinct materials to form prescribed initial states, and use thermal annealing to evolve these manifestly non-equilibrium states through the assembly landscape, traversing normally inaccessible transient structures. We explore the enormous associated hyperspace, spanning processing (annealing temperature and time), material (composition and molecular weight), and layering (thickness and order) dimensions. We demonstrate a library of exotic non-native morphologies, including vertically-oriented perforated lamellae, aqueduct structures (vertical lamellar walls with substrate-pinned perforations), parapets (crenellated lamellae), and networks of crisscrossing lamellae. This enhanced structural control can be used to modify functional properties, including accessing regimes that surpass their equilibrium analogs.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Human CD4-binding site antibody elicited by polyvalent DNA prime-protein boost vaccine neutralizes cross-clade tier-2-HIV strains

The vaccine elicitation of HIV tier-2-neutralization antibodies has been a challenge. Here, we report the isolation and characterization of a CD4-binding site (CD4bs) specific monoclonal antibody, HmAb64, from a human volunteer immunized with a polyvalent DNA prime-protein boost HIV vaccine. HmAb64 is derived from heavy chain variable germline gene IGHV1-18 and light chain germline gene IGKV1-39. It has a third heavy chain complementarity-determining region (CDR H3) of 15 amino acids. On a cross-clade panel of 208 HIV-1 pseudo-virus strains, HmAb64 neutralized 20 (10%), including tier-2 strains from clades B, BC, C, and G. The cryo-EM structure of the antigen-binding fragment of HmAb64 in complex with a CNE40 SOSIP trimer revealed details of its recognition; HmAb64 uses both heavy and light CDR3s to recognize the CD4-binding loop, a critical component of the CD4bs. This study demonstrates that a gp120-based vaccine can elicit antibodies capable of tier 2-HIV neutralization.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Mechanism of RanGTP priming H2A-H2B release from Kap114 in an atypical RanGTP•Kap114•H2A-H2B complex

Previously, we showed that the nuclear import receptor Importin-9 wraps around the H2A-H2B core to chaperone and transport it from the cytoplasm to the nucleus. However, unlike most nuclear import systems where RanGTP dissociates cargoes from their importins, RanGTP binds stably to the Importin-9•H2A-H2B complex, and formation of the ternary RanGTP•Importin-9•H2A-H2B complex facilitates H2A-H2B release to the assembling nucleosome. It was unclear how RanGTP and the cargo H2A-H2B can bind simultaneously to an importin, and how interactions of the three components position H2A-H2B for release. Here, we show cryo-EM structures of Importin-9•RanGTP and of its yeast homolog Kap114, including Kap114•RanGTP, Kap114•H2A-H2B, and RanGTP•Kap114•H2A-H2B, to explain how the conserved Kap114 binds H2A-H2B and RanGTP simultaneously and how the GTPase primes histone transfer to the nucleosome. In the ternary complex, RanGTP binds to the N-terminal repeats of Kap114 in the same manner as in the Kap114/Importin-9•RanGTP complex, and H2A-H2B binds via its acidic patch to the Kap114 C-terminal repeats much like in the Kap114/Importin-9•H2A-H2B complex. Ran binds to a different conformation of Kap114 in the ternary RanGTP•Kap114•H2A-H2B complex. Here, Kap114 no longer contacts the H2A-H2B surface proximal to the H2A docking domain that drives nucleosome assembly, positioning it for transfer to the assembling nucleosome or to dedicated H2A-H2B chaperones in the nucleus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Spectroscopy of A=9 hyperlithium with the $(e,e^{\prime}K^{+})$ reaction

Missing mass spectroscopy with the $(e,e^{\prime}K^{+})$ reaction was performed at JLab Hall C for the neutron rich $\Lambda$ hypernucleus $^{9}_{\Lambda}{\rm Li}$. The ground state energy was obtained to be $B_{\Lambda}^{\rm g.s.}=8.84\pm0.17^{\rm stat.}\pm0.15^{\rm sys.}~{\rm MeV}$ by using shell model calculations of a cross section ratio and an energy separation of the spin doublet states ($3/2^{+}_1$ and $5/2^{+}_1$). In addition, peaks that are considered to be states of [$^{8}{\rm Li}(3^{+})\otimes s_{\Lambda}=3/2^{+}_{2}, 1/2^{+}$] and [$^{8}{\rm Li}(1^{+})\otimes s_{\Lambda}=5/2^{+}_{2}, 7/2^{+}$] were observed at $E_{\Lambda}(\#2)=1.74\pm0.27^{\rm stat.}\pm0.11^{\rm sys.}~{\rm MeV}$ and $E_{\Lambda}(\#3)=3.30\pm0.24^{\rm stat.}\pm0.11^{\rm sys.}~{\rm MeV}$, respectively. The $E_{\Lambda}(\#3)$ is larger than shell model predictions by a few hundred keV, and the difference would indicate that a ${\rm ^{5}He}+t$ structure is more developed for the $3^{+}$ state than those for the $2^{+}$ and $1^{+}$ states in a core nucleus $^{8}{\rm Li}$ as a cluster model calculation suggests.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

PpIX‐enabled fluorescence‐based detection and photodynamic priming of platinum‐resistant ovarian cancer cells under fluid shear stress

Over 75% percent of ovarian cancer patients are diagnosed with advanced-stage disease characterized by unresectable intraperitoneal dissemination and the presence of ascites, or excessive fluid build-up within the abdomen. Conventional treatments include cytoreductive surgery followed by multi-line platinum and taxane chemotherapy regimens. Despite an initial response to treatment, over 75% of patients with advanced-stage ovarian cancer will relapse and succumb to platinum-resistant disease. Recent evidence suggests that fluid shear stress (FSS), which results from the movement of fluid such as ascites, induces epithelial-to-mesenchymal transition and confers resistance to carboplatin in ovarian cancer cells. This study demonstrates, for the first time, that FSS-induced platinum resistance correlates with increased cellular protoporphyrin IX (PpIX), the penultimate downstream product of heme biosynthesis, the production of which can be enhanced using the clinically approved pro-drug aminolevulinic acid (ALA). These data suggest that, with further investigation, PpIX could serve as a fluorescence-based biomarker of FSS-induced platinum resistance. Additionally, this study investigates the efficacy of PpIX-enabled photodynamic therapy (PDT) and the secretion of extracellular vesicles under static and FSS conditions in Caov-3 and NIH:OVCAR-3 cells, two representative cell lines for high-grade serous ovarian carcinoma (HGSOC), the most lethal form of the disease. FSS induces resistance to ALA-PpIX-mediated PDT, along with a significant increase in the number of EVs. Finally, the ability of PpIX-mediated photodynamic priming (PDP) to enhance carboplatin efficacy under FSS conditions is quantified. These preliminary findings in monolayer cultures necessitate additional studies to determine the feasibility of PpIX as a fluorescence-based indicator, and mediator of PDP, to target chemoresistance in the context of FSS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Jasmonate primes plant responses to extracellular ATP

SUMMARYExtracellular ATP (eATP) signaling in Arabidopsis thaliana is mediated by the purinoceptor P2K1. Previous studies have clarified that the downstream transcriptional responses to eATP involve jasmonate (JA)‐based signaling components such as the JA receptor (COI1) and JA‐responsive bHLH transcription factors (MYCs). However, the specific contributions of JA itself on eATP signaling are unexplored. Here, we report that JA primes plant responses to eATP through P2K1. Our findings show that JA treatment significantly upregulates P2K1 transcription, corroborating our observation that JA facilitates eATP‐induced cytosolic calcium elevation and transcriptional reprogramming in a JA signaling‐dependent manner. Additionally, we find that salicylic acid pre‐treatment represses eATP‐induced plant response. These results suggest that JA accumulation during biotic or abiotic stresses potentiates eATP signaling, enabling plants to better cope with subsequent stress events.

Jewell, Jeremy B. [Institute of Biological Chemist↗
DOE OSTI2025

Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second-strand nicking

R2 retrotransposons are site-specific eukaryotic non–long terminal repeat retrotransposons that copy and paste into gene loci encoding ribosomal RNAs. Recently, we demonstrated that avian A-clade R2 proteins achieve efficient and precise insertion of transgenes into their native safe-harbor loci in human cells. The features of A-clade R2 proteins that support gene insertion are not well characterized. Here, we report high-resolution cryo–electron microscopy structures of two vertebrate A-clade R2 proteins at the initiation of target-primed reverse transcription and after cDNA synthesis and second-strand nicking. Using biochemical and cellular assays, we illuminate the basis for high selectivity of template use and unique roles for each of the three zinc-finger domains in nucleic acid recognition. Reverse transcriptase active site architecture is reinforced by an unanticipated insertion motif specific to vertebrate A-clade R2 proteins. Our work provides the first insights into A-clade R2 protein structure during gene insertion and may enable future improvement and adaptation of R2-based systems for precise transgene insertion.

Science & Technology - Other Topics↗
DOE OSTI2021

PRIME

SAND2021-0565 O PRIME is a modeling framework designed for the real-time characterization and forecasting of partially observed epidemics. The method is designed to help guide medical resource allocation in the early epoch of the outbreak. Characterization is the estimation of infection spread parameters using daily counts of symptomatic patients. The estimation problem is posed as one of Bayesian inference and solved using a Markov Chain Monte Carlo technique. The framework can accommodate multiple epidemic waves and can help identify different disease dynamics at the regional, state, and country levels. Examples are provided using publicly available COVID-19 data. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Safta, Cosmin↗
DOE OSTI2024

Prime VI

SAND2025-03757O Prime VI is a distribution-of-disease outbreak model calibration code based on variational inference. It accompanies a publication for submission to Statistics in Medicine journal, and the code will be maintained for open-source use on Sandia's GitLab. The software provides methods for calibrating an epidemiological model to measured case-count data for a multitude of correlated spatial regions. The code solves a Bayesian inverse problem for model calibration where the posterior over-model parameters are approximated through a custom implementation of variational inference. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Safta, Cosmin↗
DOE OSTI2024

PCAST: Joint Statement to Leaders from the United States' President's Council of Advisors on Science and Technology and United Kingdom's Prime Minister's Council for Science and Technology

The President’s Council of Advisors on Science and Technology (PCAST) is the sole body of advisors from outside the federal government charged with making science, technology, and innovation policy recommendations to the President and the White House. Established by Executive Order, it is an independent Federal Advisory Committee comprised of distinguished individuals from industry, academia, and non-profit organizations with a range of perspectives and expertise. On March 14, 2024, PCAST and the UK Council for Science and Technology sent a joint letter to President Biden and Prime Minister Sunak outlining shared priorities for ongoing collaboration and the sharing of expertise between the two Councils.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

PRIME - A Software Toolkit for the Characterization of Partially Observed Epidemics in a Bayesian Framework

PRIME is a modeling framework designed for the “real-time’” characterization and forecasting of partially observed epidemics. Characterization is the estimation of infection spread parameters using daily counts of symptomatic patients. The method is designed to help guide medical resource allocation in the early epoch of the outbreak. The estimation problem is posed as one of Bayesian inference and solved using a Markov Chain Monte Carlo technique. The framework can accommodate multiple epidemic waves and can help identify different disease dynamics at the regional, state, and country levels. We include examples using publicly available COVID-19 data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A Joint Search for the Electromagnetic Counterpart to the Gravitational-Wave Binary Black-Hole Merger Candidate S250328ae with the Dark Energy Camera and the Prime Focus Spectrograph

The first detection of an optical counterpart to a gravitational wave signal revealed that collaborative efforts between instruments with different specializations provide a unique opportunity to acquire impactful multi-messenger data. We present results of such a joint search with the Dark Energy Camera (DECam) and Prime Focus Spectrograph (PFS) for the optical counterpart of the LIGO-Virgo-KAGRA event S250328ae, a binary black hole merger candidate of high significance detected at a distance of 511$\pm$82 Mpc and localized within an area of 3 (15) square degrees at 50% (90%) confidence. We observed the 90% confidence area with DECam and identified 36 high-confidence transient candidates after image processing, candidate selection, and candidate vetting. We observed with PFS to obtain optical spectra of DECam candidates, Swift-XRT candidates, and potential host galaxies of S250328ae. In total, 3897 targets were observed by seven pointings covering ~50% of the 90% confidence area. After template fitting and visual inspection, we identified 12 SNe, 159 QSOs, 2975 galaxies, and 131 stars. With the joint observations of DECam and PFS, we found variability in 12 SNe, 139 QSOs, 37 galaxies, and 2 stars. We do not identify any confident optical counterparts, though the association is not ruled out for three variable candidates that are not observed by PFS and 6 QSO candidates without clear variability if the optical counterpart of S250328ae is faint. Despite the lack of confident optical counterparts, this paper serves as a framework for future collaborations between wide-field imagers and multi-object spectrographs to maximize multi-messenger analyses.

Zhang, Haibin [Natl. Astron. Observ. of Japan] (OR↗
DOE OSTI2021

Priming mechanisms providing plants and microbes access to mineral-associated organic matter

Mineral-associated organic matter (MAOM) is considered a stable reservoir for soil nutrients that influences long-term soil carbon (C) and nitrogen (N) dynamics. However, recent experimental and theoretical evidence shows that root exudates may mobilize MAOM, thereby providing plants and microbes access to a large and N-rich pool. Given the mechanisms underlying MAOM C and N mobilization remain largely untested, we examined direct and indirect pathways by which root exudates destabilize this nutrient pool in laboratory mesocosms. We simulated root exudation with 13 C-labeled oxalic acid to test whether root exudates are directly capable of mobilizing MAOM from mineral surfaces; and with 13 C-labeled glucose to test whether indirect stimulation of microbial and extracellular enzyme activity leads to MAOM decomposition. We also tested the potential for oxalic acid and glucose to mobilize MAOM in an additional subset of sterilized soils to clarify the potential for non-microbial pathways of MAOM destabilization. Over the course of the 12-day MAOM incubation with and without simulated exudates, we measured C cycling (CO 2 respiration rates, 13 C–CO 2 efflux), N cycling (inorganic N pools, gross N mineralization) and related microbial processes (enzyme activities and microbial community composition via phospholipid fatty acid analysis). Both of the simulated root exudates enhanced MAOM-C mineralization, with cumulative respiration increasing 35–89% relative to the water-only control. Likewise, glucose additions enhanced the production of an exo-cellulase and a chitinase by up to 130% and 39%, respectively, while oxalic acid enhanced oxidative enzyme activities up to 91% greater than control rates. We observed a positive association between glucose-induced shifts in enzyme activities, MAOM-C mineralization, and gross ammonification. Oxalic acid additions were associated with initial increases in fungal relative abundance and in sterile soils appeared to stimulate the release of metals and dissolved organic nitrogen into exchangeable pools. Our results indicate that common root exudates, like glucose and oxalic acid, can significantly increase the turnover and potential release of C and N from MAOM through indirect (e.g., enzyme induction) and direct (e.g., mobilization of metal oxides) mechanisms.

54 ENVIRONMENTAL SCIENCES↗