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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Editorial: Towards the rapid and systematic assessment of vaccine technologies

The COVID-19 pandemic highlighted both the extraordinary potential of modern vaccinology and persistent challenges in how vaccine technologies are assessed. While vaccines can be developed and deployed at unprecedented speed, our ability to predict efficacy in a population is constrained by methodological difficulties, underreporting of negative results, and limited comparability across studies. This editorial introduces a Research Topic that brings together an interdisciplinary collection of experimental, computational, and theoretical contributions spanning multiple pathogens and vaccine platforms. Across these contributions, emerging themes emphasize the need for standardized immunogenicity metrics, transparent reporting including negative findings, and harmonized experimental protocols to support meaningful comparisons. This editorial highlights community practices and shared commitments – supported by researchers, funders, and journals – that could strengthen reproducibility, transparency, and cumulative learning in vaccine research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Rapid Construction of an Infectious Clone of the Zika Virus, Strain ZKC2

Zika virus (ZIKV) has had detrimental effects on global public health in recent years. This is because the management of the disease has been limited, in part because its pathogenic mechanisms are not yet completely understood. Infectious clones are an important tool that utilize reverse genetics; these can be used to modify the ZIKV genomic RNA at the DNA level. A homologous recombination clone was used to construct pWSK29, a low copy plasmid that contained sequences for a T7 promoter, the whole genome of ZIKV ZKC2 strain, and a hepatitis delta virus ribozyme. High fidelity PCR was then used to amplify the T7 transcription template. The transcript was then transfected into susceptible cells via lipofection to recover the ZIKV ZKC2 strain. Finally, the virulence of rZKC2 was evaluated both in vitro and in vivo . The rZKC2 was successfully obtained and it showed the same virulence as its parent, the ZIKV ZKC2 strain (pZKC2), both in vitro and in vivo . The 3730 (NS2A-D62G) mutation site was identified as being important, since it had significant impacts on rZKC2 recovery. The 4015 (NS2A, A157V) mutation may reduce virus production by increasing the interferon type I response. In this study, one of the earliest strains of ZIKV that was imported into China was used for infectious clone construction and one possible site for antiviral medication development was discovered. The use of homologous recombination clones, of PCR products as templates for T7 transcription, and of lipofection for large RNA transfection could increase the efficiency of infectious clone construction. Our infectious clone provides an effective tool which can be used to explore the life cycle and medical treatment of ZIKV.

Qin, Zhiran↗
DOE OSTI2023

Wounding rapidly alters transcription factor expression, hormonal signaling, and phenolic compound metabolism in harvested sugarbeet roots

Injuries sustained by sugarbeet (Beta vulgaris L.) roots during harvest and postharvest operations seriously reduce the yield of white sugar produced from stored roots. Although wound healing is critically important to reduce losses, knowledge of these processes is limited for this crop as well as for roots in other species. To better understand the metabolic signals and changes that occur in wounded roots, dynamic changes in gene expression were determined by RNA sequencing and the activity of products from key genes identified in this analysis were determined in the 0.25 to 24 h following injury. Nearly five thousand differentially expressed genes that contribute to a wide range of cellular and molecular functions were identified in wounded roots. Highly upregulated genes included transcription factor genes, as well as genes involved in ethylene and jasmonic acid (JA) biosynthesis and signaling and phenolic compound biosynthesis and polymerization. Enzyme activities for key genes in ethylene and phenolic compound biosynthesis and polymerization also increased due to wounding. Results indicate that wounding causes a major reallocation of metabolism in sugarbeet taproots. Although both ethylene and JA are likely involved in triggering wound responses, the greater and more sustained upregulation of ethylene biosynthesis and signaling genes relative to those of JA, suggest a preeminence of ethylene signaling in wounded sugarbeet roots. Changes in gene expression and enzymes involved in phenolic compound metabolism additionally indicate that barriers synthesized to seal off wounds, such as suberin or lignin, are initiated within the first 24 h after injury.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

PARA: A New Platform for the Rapid Assembly of gRNA Arrays for Multiplexed CRISPR Technologies

Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dioxin-Linked Covalent Organic Framework-Supported Palladium Complex for Rapid Room-Temperature Suzuki–Miyaura Coupling Reaction

Covalent organic framework (COF)-supported palladium catalysts have garnered enormous attention for cross-coupling reactions. However, the limited linkage types in COF hosts and their suboptimal catalytic performance have hindered their widespread implementation. Herein, we present the first study immobilizing palladium acetate onto a dioxin-linked COF (Pd/COF-318) through a facile solution impregnation approach. By virtue of its permanent porosity, accessible Pd sites arranged in periodic skeletons, and framework robustness, the resultant Pd/COF-318 exhibits exceptionally high activity and broad substrate scope for the Suzuki–Miyaura coupling reaction between aryl bromides and arylboronic acids at room temperature within an hour, rendering it among the most effective Pd/COF catalysts for Suzuki–Miyaura coupling reactions to date. Moreover, Pd/COF-318 demonstrates excellent recyclability, retaining high activity over five cycles without significant deactivation. The leaching test confirms the heterogeneity of the catalyst. This work uncovers the vast potential of dioxin-linked COFs as catalyst supports for highly active, selective, and durable organometallic catalysis.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The Effect of Rapid Development on Soil CO2 Efflux in a Cellulosic Biofuel Stand

As awareness of climate change increases, the need for carbon neutral fuel sources is growing. Lignocellulosic biofuel derived from pine trees has been suggested as one potential energy source; however, it requires more research before its efficacy for climate change mitigation can be determined. Due to the large share of forest carbon held in soils and the extensive area of pine plantations in the southeast U.S., a better understanding of plantation soil carbon dynamics is critical for biofuel carbon accounting. This study evaluated the effects of canopy development and productivity on soil CO2 efflux, a proxy for soil respiration (Rs), in an intensively managed loblolly pine (Pinus taeda) stand over a period from May 2015 to December 2019. We found that leaf area index (LAI) and gross ecosystem production (GEP), as well as meteorological variables, had significant effects on Rs, but that both overall Rs and soil carbon pools did not increase over the course of the study. We thus hypothesize that GEP and LAI had intra-annual effects on Rs, and that the lack of change in Rs is the result of an increase in autotrophic respiration (Ra) that offset a decrease in decomposition of the previous stand’s organic matter.

09 BIOMASS FUELS↗
DOE OSTI2023

Utilization of Additive Manufacturing for the Rapid Prototyping of C-Band Radiofrequency Loads

Additive manufacturing is a versatile technique that shows promise in providing quick and dynamic manufacturing for complex engineering problems. Research has been ongoing into the use of additive manufacturing for potential applications in radiofrequency (RF) component technologies. Here, we present a method for developing an effective prototype load produced from 316L stainless steel on a direct metal laser sintering machine. The model was tested using simulation software to verify the validity of the design. The load structure was manufactured by an online digital manufacturing company, showing the viability of using easily accessible tools to manufacture RF structures. The produced load was able to produce an S11 value of −22.8 dB at a C-band frequency of 5.712 GHz while under a vacuum. In a high-power test, the load was able to terminate a peak power of 8.1 MW. The discussion includes future applications of the present method and how it will help to improve the implementation of future accelerator concepts.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Active Learning for Rapid Targeted Synthesis of Compositionally Complex Alloys

The next generation of advanced materials is tending toward increasingly complex compositions. Synthesizing precise composition is time-consuming and becomes exponentially demanding with increasing compositional complexity. An experienced human operator does significantly better than a novice but still struggles to consistently achieve precision when synthesis parameters are coupled. The time to optimize synthesis becomes a barrier to exploring scientifically and technologically exciting compositionally complex materials. This investigation demonstrates an active learning (AL) approach for optimizing physical vapor deposition synthesis of thin-film alloys with up to five principal elements. We compared AL-based on Gaussian process (GP) and random forest (RF) models. The best performing models were able to discover synthesis parameters for a target quinary alloy in 14 iterations. We also demonstrate the capability of these models to be used in transfer learning tasks. RF and GP models trained on lower dimensional systems (i.e., ternary, quarternary) show an immediate improvement in prediction accuracy compared to models trained only on quinary samples. Furthermore, samples that only share a few elements in common with the target composition can be used for model pre-training. We believe that such AL approaches can be widely adapted to significantly accelerate the exploration of compositionally complex materials.

Chemistry↗
DOE OSTI2023

Real-Time and Rapid Respiratory Response of the Soil Microbiome to Moisture Shifts

Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry–rewet events occurs sequentially at different rates. We amended desiccated soils with 13 C-labeled glucose and measured the rates of 12 CO 2 and 13 CO 2 respiration in real time after rewetting. Using these differentiated 12 CO 2 and 13 CO 2 respiration rate soils after rewetting, we were able to deduce when microbes are accessing different pools of carbon. Immediately upon rewetting, respiration of 12 CO 2 occurred first, with negligible 13 CO 2 respiration. Appreciable metabolism and respiration of the added 13 C glucose did not occur until 15 min after rewetting. We conclude that, while all carbon pools are being accessed in the first 9 h after rewetting, the rate and timing at which new and existing carbon pools are being accessed varies. Within this study, using stable isotope-labeled substrates to discern which carbon pools are metabolized first uniquely illustrates how microorganisms access different carbon pools which has implications into understanding how carbon metabolism can further affect climate, carbon sequestration, and soil health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Accelerator-Based Production of Scandium Radioisotopes for Applications in Prostate Cancer: Toward Building a Pipeline for Rapid Development of Novel Theranostics

In the field of nuclear medicine, the β + -emitting 43 Sc and β - -emitting 47 Sc are promising candidates in cancer diagnosis and targeted radionuclide therapy (TRT) due to their favorable decay schema and shared pharmacokinetics as a true theranostic pair. Additionally, scandium is a group-3 transition metal (like 177 Lu) and exhibits affinity for DOTA-based chelators, which have been studied in depth, making the barrier to implementation lower for 43/47 Sc than for other proposed true theranostics. Before 43/47 Sc can see widespread pre-clinical evaluation, however, an accessible production methodology must be established and each isotope’s radiolabeling and animal imaging capabilities studied with a widely utilized tracer. As such, a simple means of converting an 18 MeV biomedical cyclotron to support solid targets and produce 43 Sc via the 42 Ca(d,n) 43 Sc reaction has been devised, exhibiting reasonable yields. The Nat Ti(γ,p) 47 Sc reaction is also investigated along with the successful implementation of chemical separation and purification methods for 43/47 Sc. The conjugation of 43/47 Sc with PSMA-617 at specific activities of up to 8.94 MBq/nmol and the subsequent imaging of LNCaP-ENZaR tumor xenografts in mouse models with both 43/47 Sc-PSMA-617 are also presented.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

A Rapid and High Throughput MIC Determination Method to Screen Uranium Resistant Microorganisms

The assessment of minimum inhibitory concentration (MIC) is a conventional technique used for the screening of microbial resistance against antibiotics, biocides, and contaminants such as heavy metals. However, as part of our ongoing work, we have observed biases associated with using traditional liquid MIC method to screen microbial heavy metal resistance, including both bacterial and fungal strains. Specifically, the addition of uranium into synthetic media causes immediate precipitation prior to the initiation of microbial growth, thus hampering the optical density measurements, and the obtained MIC values are thus flawed and inaccurate. To address this discrepancy, we report the optimization and development of a serial-dilution-based MIC method conducted on solid growth media supplemented with uranium, which is more accurate, relative to the testing of MICs performed in liquid cultures. Notably, we report on the efficacy of this method to screen not only bacteria that are resistant to uranium but also demonstrate the successful application to yeast and fungal isolates, for their ability to resist uranium, is more accurate and sensitive relative to the liquid method. We believe that this newly developed method to screen heavy metal resistance, such as uranium, is far superior to the existing liquid MIC method and propose replacing the liquid assay with the solid plate MIC reported herein.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A Rapid Method for Detecting Normal or Modified Plant and Algal Carbonic Anhydrase Activity Using Saccharomyces cerevisiae

In recent years, researchers have attempted to improve photosynthesis by introducing components from cyanobacterial and algal CO2-concentrating mechanisms (CCMs) into terrestrial C3 plants. For these attempts to succeed, we need to understand the CCM components in more detail, especially carbonic anhydrase (CA) and bicarbonate (HCO3−) transporters. Heterologous complementation systems capable of detecting carbonic anhydrase activity (i.e., catalysis of the pH-dependent interconversion between CO2 and HCO3−) or active HCO3− transport can be of great value in the process of introducing CCM components into terrestrial C3 plants. In this study, we generated a Saccharomyces cerevisiae CA knock-out (ΔNCE103 or ΔCA) that has a high-CO2-dependent phenotype (5% (v/v) CO2 in air). CAs produce HCO3− for anaplerotic pathways in S. cerevisiae; therefore, the unavailability of HCO3− for neutral lipid biosynthesis is a limitation for the growth of ΔCA in ambient levels of CO2 (0.04% (v/v) CO2 in air). ΔCA can be complemented for growth at ambient levels of CO2 by expressing a CA from human red blood cells. ΔCA was also successfully complemented for growth at ambient levels of CO2 through the expression of CAs from Chlamydomonas reinhardtii and Arabidopsis thaliana. The ΔCA strain is also useful for investigating the activity of modified CAs, allowing for quick screening of modified CAs before putting them into the plants. CA activity in the complemented ΔCA strains can be probed using the Wilbur–Anderson assay and by isotope exchange membrane-inlet mass spectrometry (MIMS). Other potential uses for this new ΔCA-based screening system are also discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Variable X-Ray Reverberation in the Rapidly Accreting Active Galactic Nucleus Ark 564: The Response of the Soft Excess to the Changing Geometry of the Inner Accretion Flow

X-ray reverberation, which exploits the time delays between variability in different energy bands as a function of Fourier frequency, probes the structure of the inner accretion disks and X-ray coronae of active galactic nuclei. We present a systematic X-ray spectroscopic and reverberation study of the high-Eddington-ratio narrow-line Seyfert 1 galaxy Ark 564, using over 900 ks of XMM-Newton and NuSTAR observations spanning 13 yr. The time-averaged spectra can be well described by a model consisting of a coronal continuum, relativistic disk reflection, warm Comptonization, and three warm absorbers. Leveraging the high X-ray brightness of Ark 564, we are able to resolve the time evolution of the spectra and contemporaneous reverberation lags. The soft-band lag relative to the continuum increases with the X-ray flux, while Fe Kα lags are detected in only a subset of epochs and do not correlate with soft lags. Models based on a lamppost corona and reflection from a standard thin disk can broadly reproduce the observed lag-energy spectra of low-flux epochs; however, additional reverberation from the warm Comptonized atmosphere is required to explain the soft lags observed in high-flux epochs. A vertically puffed-up inner disk and a variable, vertically extended corona can better explain the observed evolution of the lags and covariance spectra. Our study underscores the importance of multiepoch, multiband analyses for a comprehensive understanding the inner accretion disk and corona.

Active galactic nuclei↗
DOE OSTI2022

Electromagnetic Fireworks: Fast Radio Bursts from Rapid Reconnection in the Compressed Magnetar Wind

One scenario for the generation of fast radio bursts (FRBs) is magnetic reconnection in a current sheet of the magnetar wind. Compressed by a strong magnetic pulse induced by a magnetar flare, the current sheet fragments into a self-similar chain of magnetic islands. Time-dependent plasma currents at their interfaces produce coherent radiation during their hierarchical coalescence. We investigate this scenario using 2D radiative relativistic particle-in-cell simulations to compute the efficiency of the coherent emission and to obtain frequency scalings. Consistent with expectations, a fraction of the reconnected magnetic field energy, f ~ 0.002, is converted to packets of high-frequency fast magnetosonic waves, which can escape from the magnetar wind as radio emission. In agreement with analytical estimates, we find that magnetic pulses of 10 47 erg s –1 can trigger relatively narrowband GHz emission with luminosities of approximately 10 42 erg s –1 , sufficient to explain bright extragalactic FRBs. The mechanism provides a natural explanation for a downward frequency drift of burst signals, as well as the ~100 ns substructure recently detected in FRB 20200120E.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Rapid evolution of aerosol particles and their optical properties downwind of wildfires in the western US

Abstract. During the first phase of the Biomass Burn Operational Project (BBOP) field campaign, conducted in the Pacific Northwest, the DOE G-1 aircraft was used to follow the time evolution of wildfire smoke from near the point of emission to locations 2–3.5 h downwind. In nine flights we made repeated transects of wildfire plumes at varying downwind distances and could thereby follow the plume's time evolution. On average there was little change in dilution-normalized aerosol mass concentration as a function of downwind distance. This consistency hides a dynamic system in which primary aerosol particles are evaporating and secondary ones condensing. Organic aerosol is oxidized as a result. On all transects more than 90 % of aerosol is organic. In freshly emitted smoke aerosol, NH4+ is approximately equivalent to NO3. After 2 h of daytime aging, NH4+ increased and is approximately equivalent to the sum of Cl, SO42, and NO3. Particle size increased with downwind distance, causing particles to be more efficient scatters. Averaged over nine flights, mass scattering efficiency (MSE) increased in ∼ 2 h by 56 % and doubled in one flight. Mechanisms for redistributing mass from small to large particles are discussed. Coagulation is effective at moving aerosol from the Aitken to accumulation modes but yields only a minor increase in MSE. As absorption remained nearly constant with age, the time evolution of single scatter albedo was controlled by age-dependent scattering. Near-fire aerosol had a single scatter albedo (SSA) of 0.8–0.9. After 1 to 2 h of aging SSAs were typically 0.9 and greater. Assuming global-average surface and atmospheric conditions, the observed age dependence in SSA would change the direct radiative effect of a wildfire plume from near zero near the fire to a cooling effect downwind.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Rapid saturation of cloud water adjustments to shipping emissions

Abstract. Human aerosol emissions change cloud properties by providing additional cloud condensation nuclei. This increases cloud droplet numbers, which in turn affects other cloud properties like liquid-water content and ultimately cloud albedo. These adjustments are poorly constrained, making aerosol effects the most uncertain part of anthropogenic climate forcing. Here we show that cloud droplet number and water content react differently to changing emission amounts in shipping exhausts. We use information about ship positions and modeled emission amounts together with reanalysis winds and satellite retrievals of cloud properties. The analysis reveals that cloud droplet numbers respond linearly to emission amount over a large range (1–10 kg h−1) before the response saturates. Liquid water increases in raining clouds, and the anomalies are constant over the emission ranges observed. There is evidence that this independence of emissions is due to compensating effects under drier and more humid conditions, consistent with suppression of rain by enhanced aerosol. This has implications for our understanding of cloud processes and may improve the way clouds are represented in climate models, in particular by changing parameterizations of liquid-water responses to aerosol.

54 ENVIRONMENTAL SCIENCES↗