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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation

Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics data set from 48 bacterial strains representing six phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, including those involved in central carbon metabolism and translation. Among the proteins with the most conserved methylation sites is ribosomal protein L11 (bL11). bL11 methylation has been a mystery for five decades, as the deletion of its methyltransferase PrmA causes no cell growth defects. Comparative proteomics analysis combined with inorganic polyphosphate and guanosine tetra/pentaphosphate assays of the ΔprmA mutant in Escherichia coli revealed that bL11 methylation is important for stringent response signaling. In the stationary phase, we found that the ΔprmA mutant has impaired guanosine tetra/pentaphosphate production. This leads to a reduction in inorganic polyphosphate levels, accumulation of RNA and ribosomal proteins, and an abnormal polysome profile. Overall, our investigation demonstrates that the evolutionarily conserved bL11 methylation is important for stringent response signaling and ribosomal activity regulation and turnover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Triggering the stringent response enhances synthetic methanol utilization in Escherichia coli

Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, i.e. the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here in this paper, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. By activating the stringent/stress response via ppGpp overproduction, or DksA and RpoS overexpression, we demonstrate improved biosynthesis of proteinogenic amino acids via endogenous upregulation of amino acid synthesis pathway genes. Thus, we were able to achieve biosynthesis of several limiting amino acids from methanol-derived carbon, in contrast to the control methylotrophic E. coli strain. This study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via stringent/stress response activation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗
DOE OSTI2022

Expression and structure of the Chlamydia trachomatis DksA ortholog

Chlamydia trachomatis is a bacterial obligate intracellular parasite and a significant cause of human disease, including sexually transmitted infections and trachoma. The bacterial RNA polymerase-binding protein DksA is a transcription factor integral to the multicomponent bacterial stress response pathway known as the stringent response. The genome of C. trachomatis encodes a DksA ortholog (DksA Ct ) that is maximally expressed at 15–20 h post infection, a time frame correlating with the onset of transition between the replicative reticulate body (RB) and infectious elementary body (EB) forms of the pathogen. Ectopic overexpression of DksA Ct in C. trachomatis prior to RB–EB transitions during infection of HeLa cells resulted in a 39.3% reduction in overall replication (yield) and a 49.6% reduction in recovered EBs. While the overall domain organization of DksA Ct is similar to the DksA ortholog of Escherichia coli (DksA Ec ), DksA Ct did not functionally complement DksA Ec . Transcription of dksA Ct is regulated by tandem promoters, one of which also controls expression of nrdR, encoding a negative regulator of deoxyribonucleotide biosynthesis. The phenotype resulting from ectopic expression of DksA Ct and the correlation between dksA Ct and nrdR expression is consistent with a role for DksA Ct in the C. trachomatis developmental cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

CRISPRt data studying the physiological role of an Acinetobacter-specific sigma factor

Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE. We combine promoter mutagenesis, motif scanning, and ChIP-seq to define the direct SigAb regulon, which consists of sigAb itself, the stringent response mediator, relA, and the uncharacterized small RNA, "sabS."

Peters, Jason M. [GLBRC - University of Wisconsin]↗
DOE OSTI2025

Physiological roles of an Acinetobacter -specific σ factor

ABSTRACT The Gram-negative pathogen Acinetobacter baumannii is considered an “urgent threat” to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF “SigAb”; however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE-like ECFs. We combine promoter mutagenesis, motif scanning, and chromatin immunoprecipitation-sequencing (ChIP-seq) to define the direct SigAb regulon, which consists of genes encoding SigAb itself, the stringent response mediator, RelA, and the uncharacterized small RNA, “SabS.” However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper-induced SigAb-dependent transcription. Furthermore, we found that two uncharacterized genes in the sigAb operon, “ aabA ” and “ aabB ,” have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb , aabA , and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii . IMPORTANCE Acinetobacter baumannii is a hospital-acquired pathogen, and many strains are resistant to multiple antibiotics. Understanding how A. baumannii senses and responds to stress may uncover novel routes to treat infections. Here, we examine how the Acinetobacter -specific transcription factor, SigAb, mitigates stress. We find that SigAb directly regulates only a small number of genes, but indirectly controls hundreds of genes that have substantial impacts on cell physiology. We show that SigAb is required for maximal growth, even during optimal conditions, and is acutely required during growth in the presence of elevated copper. Given that copper toxicity plays roles in pathogenesis and on copper-containing surfaces in hospitals, we speculate that SigAb function may be important in clinically relevant contexts.

Bacon, Emily E. (ORCID:0000000180907689)↗
DOE OSTI2025

Bacteria export alarmone synthetases that produce (p)ppApp and (p)ppGpp

Guanosine penta- and tetraphosphate [(p)ppGpp] and their adenosine analogs [(p)ppApp] are bacterial second messengers known as alarmones. Members of the RelA-SpoT homolog (RSH) family synthesize (p)ppGpp to mediate the stringent response during nutrient starvation, whereas (p)ppApp synthetases have been identified as bactericidal toxins in diverse contexts including type VI secretion systems, toxin-antitoxin modules, and phages. Although alarmone synthesis has traditionally been viewed as a cytoplasmic process, early studies in Streptomyces suggested the existence of secreted alarmone synthetases. Here, we identify SaEAS, an exported alarmone synthetase (EAS) from Streptomyces albidoflavus, as the long-mysterious source of extracellular alarmone synthetase activity in Streptomyces. SaEAS produces both (p)ppGpp and (p)ppApp at rates exceeding 100,000 molecules per minute and has kinetic properties adapted to low substrate environments. A broader bioinformatic survey reveals ~600 EASs linked to a range of specialized bacterial secretion systems. Characterization of two additional EASs, VpEAS from Vibrio parahaemolyticus and AaEAS from Amycolatopsis azurea, shows that both produce (p)ppGpp exclusively and inhibit bacterial growth when localized to the cytoplasm. These findings challenge the longstanding view of (p)ppGpp as strictly pro-survival and unveil a diverse family of secreted RSH enzymes with potential roles in interbacterial antagonism and environmental signaling.

Ahmad, Shehryar↗
DOE OSTI2024

Vaccination induces broadly neutralizing antibody precursors to HIV gp41

A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Evaluation of the Performance and Exhaust Emissions of a 4 Cylinder CI Engine Operating With Dimethyl Ether (DME) and Propane Blends

In response to stringent emissions regulations and the need for higher efficiency engines, the utilization of DME and propane fuel blends in compression ignition (CI) engines has gained interest in the automotive industry. In this study, a range of DME-propane blends are explored in a CI combustion strategy at high injection pressures. A GT-Power model of a 2.2 L Hyundai CI engine was developed to facilitate evaluation of the impacts of variations of DME and propane blends at a light and medium engine speed-torque-load operating condition; specifically at 1500 rpm, 50 Nm and 2.84 bar brake mean effective pressure (BMEP); and 2000 rpm, 150 Nm, 8.53 bar BMEP speed-torque-load combination. Here, the GT-Power model was validated using Computational Fluid Dynamics (CFD) simulations. The results indicate that high diesel-like efficiencies can be achieved with a 100% DME mass substitution and up to 50% propane-DME blends could be implemented without a significant penalty on engine performance indicators. Significant brake specific nitrogen oxides (BSNOx) reductions were also observed along with reductions in carbon dioxide (CO2) and soot when leveraging these fuel blends.

computational fluid dynamics↗
DOE OSTI2020

Tailoring a Global Iron Regulon to a Uropathogen

Pathogenicity islands and plasmids bear genes for pathogenesis of various Escherichia coli pathotypes. Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here, we dissected a regulatory network directed by the conserved iron homeostasis regulator, ferric uptake regulator (Fur), in uropathogenic E. coli (UPEC) strain CFT073. Comparing anaerobic genome-scale Fur DNA binding with Fur-dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655 showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O 2 -dependent synthesis of the siderophore aerobactin, encoded by an operon within a pathogenicity island. Taken together, these data suggest that in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O 2 to produce aerobactin. IMPORTANCE Host iron restriction is a common mechanism for limiting the growth of pathogens. We compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E. coli K-12 to uncover strategies that pathogenic bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important in controlling growth and survival under nutrient-limiting conditions and during transitions from the nutrient-rich environment of the lower gastrointestinal (GI) tract to the more restrictive environment of the urinary tract. The coupling of the response of iron limitation to increased demand for amino acids could be a critical attribute that sets UPEC apart from other E. coli pathotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Low-threshold response of a scintillating xenon bubble chamber to nuclear and electronic recoils

A device filled with pure xenon first demonstrated the ability to operate simultaneously as a bubble chamber and scintillation detector in 2017. Initial results from data taken at thermodynamic thresholds down to ∼4 keV showed sensitivity to ∼20 keV nuclear recoils with no observable bubble nucleation by 𝛾-ray interactions. Here, this paper presents results from further operation of the same device at thermodynamic thresholds as low as 0.50 keV, hardware limited. The bubble chamber has now been shown to have sensitivity to ∼1 keV nuclear recoils while remaining insensitive to bubble nucleation by 𝛾-rays. A data-driven calibration of the chamber’s nuclear recoil nucleation response, as a function of nuclear recoil energy and thermodynamic state, is presented. Stringent upper limits are established for the probability of bubble nucleation by 𝛾-ray-induced Auger cascades, with a limit of <1.1 ×10 −6 set at 0.50 keV, the lowest thermodynamic threshold explored.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Leveraging observed soil heterotrophic respiration fluxes as a novel constraint on global-scale models

Microbially-explicit models may improve understanding and projections of carbon dynamics in response to future climate change, but their fidelity in simulating global-scale soil heterotrophic respiration (RH), a stringent test for soil biogeochemical models, has never been evaluated. We used statistical global RH products, as well as 7,821 daily site-scale RH measurements, to evaluate the spatio-temporal performance of one first-order decay model (CASA-CNP) and two microbially-explicit biogeochemical models (CORPSE and MIMICS) that were forced by two different climate datasets. CORPSE and MIMICS did not provide any measurable performance improvement; instead, the models were highly sensitive to the meteorological input data used to drive them. Spatial RH variability was generally well simulated except in the northern middle latitudes (~50°N) and arid regions; models captured the seasonal variability of RH well, but showed more divergence in tropic and arctic regions. Our results demonstrate that the next generation of biogeochemical models shows promise, but also needs to be improved for realistic spatio-temporal variability of RH. Finally, we emphasize the importance of net primary production, soil moisture, and soil temperature inputs, and that jointly evaluating soil models for their spatial (global scale) and temporal (site scale) performance provides crucial benchmarks for improving biogeochemical models.

Jian, Jinshi↗
DOE OSTI2022

Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD

Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV-2 variants of concern (VOCs). Understanding NAb epitopedependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCsandmediatestrong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinantsoftheepitope-drivenprotectionandVOCevasion.WhileEH3represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 micefrom lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Design and Performance of a Smartphone-based Cosmic Ray Observatory

This dissertation examines the feasibility of appropriating the global network of smartphones as an observatory for ultra-high-energy cosmic rays. An application and cloud-based data-acquisition system are first proposed for such an observatory, in which heterogenous devices self-calibrate and server feedback optimizes individual device triggers. Methods of monitoring and manually controlling this network are also examined. Detection efficiencies for cosmic muons, MeV-scale gamma rays, and 120 GeV protons are then measured for this trigger, with which a Monte Carlo pixel model is fine-tuned. Extending this model to cosmic ray showers, the effective area of the observatory for super-GZK primaries is shown to equal that of the Pierre Auger Observatory with a global participation rate under 0.1%, far below initial estimates presented in Ref. [83]. A vastly improved sensitivity to photons and more precise modeling of electrons are primarily responsible for this discrepancy, though more refined models of the combinatorial background may yet lead to more stringent requirements.

Swaney, Jeff↗
DOE OSTI2023

Broadband Photoconductive Sampling in Gallium Phosphide

Abstract Direct measurements of the electric field of light enable new observations of light–matter interactions. In the near‐infrared and visible spectral ranges, this typically relies on techniques that exploit nonlinearities in gases or solids, which limits their sensitivity. Here, a method for the detection of broadband near‐infrared fields spanning more than one octave from 110 to 220 THz based on linear absorption in a semiconductor is demonstrated. This technique, which avoids complex vacuum setups and works under ambient conditions, employs linear photoconductive sampling (LPS) in gallium phosphide. Simulations reveal that the response function of LPS is concerned with the intensity envelope of the gate field, in contrast to electro‐optic sampling, relaxing the stringent temporal requirements on the gate pulse.

36 MATERIALS SCIENCE↗
DOE OSTI2020

The range of non-Kitaev terms and fractional particles in α-RuCl 3

Significant efforts have focused on the magnetic excitations of relativistic Mott insulators, predicted to realize the Kitaev quantum spin liquid (QSL). This exactly solvable model involves a highly entangled state resulting from bond-dependent Ising interactions that produce excitations which are non-local in terms of spin flips. A key challenge in real materials is identifying the relative size of the non-Kitaev terms and their role in the emergence or suppression of fractional excitations. Here, we identify the energy and temperature boundaries of non-Kitaev interactions by direct comparison of the Raman susceptibility of α-RuCl 3 with quantum Monte Carlo (QMC) results for the Kitaev QSL. Moreover, we further confirm the fractional nature of the magnetic excitations, which is given by creating a pair of fermionic quasiparticles. Interestingly, this fermionic response remains valid in the non-Kitaev range. Our results and focus on the use of the Raman susceptibility provide a stringent new test for future theoretical and experimental studies of QSLs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Historic and modern nuclear graphite impurities: Pathways to improved waste strategies

Graphite has been used in large volumes as a structural material and neutron moderator since the earliest days of nuclear fission. However, no international consensus exists on the disposal of irradiated graphite, leaving much of the historic radioactive graphite inventory in interim vault or silo storage. With several new graphite-moderated reactors planned or under construction, the issue of graphite waste management is becoming increasingly urgent. This paper reviews and quantifies impurities in both historic and modern nuclear graphite, with emphasis on nitrogen—responsible for much of the 14 C inventory—and chlorine, which plays a critical role in repository performance and design. Modern graphites, benefitting from stringent quality-control measures developed for non-nuclear industries, meet or exceed the ASTM Ultra-High Purity nuclear standards, even without halide purification. Both chlorine and nitrogen concentrations have declined over time. For chlorine, identified as a key impurity influencing U.S. waste repository design, we propose a target of 0.1 appm in as-fabricated billets as a reasonable benchmark. Nitrogen sources are traced throughout the graphite production process, with surface and bulk concentrations characterized for all materials studied. Modern graphites commonly exhibit nitrogen levels below 5 appm, with values approaching 1 appm achievable. Using such reduced-nitrogen grades is critical to keeping graphite-induced radioactivity below the greater-than-Class-C waste threshold, thereby avoiding disposal cost penalties of nearly an order of magnitude.

Chlorine↗
DOE OSTI2020

2D Electrets of Ultrathin MoO 2 with Apparent Piezoelectricity

Since graphene, a variety of 2D materials have been fabricated in a quest for a tantalizing combination of properties and desired physiochemical behavior. 2D materials that are piezoelectric, i.e., that allow for a facile conversion of electrical energy into mechanical and vice versa, offer applications for sensors, actuators, energy harvesting, stretchable and flexible electronics, and energy storage, among others. Unfortunately, materials must satisfy stringent symmetry requirements to be classified as piezoelectric. Here, 2D ultrathin single-crystal molybdenum oxide (MoO 2 ) flakes that exhibit unexpected piezoelectric-like response are fabricated, as MoO 2 is centrosymmetric and should not exhibit intrinsic piezoelectricity. However, it is demonstrated that the apparent piezoelectricity in 2D MoO 2 emerges from an electret-like behavior induced by the trapping and stabilization of charges around defects in the material. Arguably, the material represents the first 2D electret material and suggests a route to artificially engineer piezoelectricity in 2D crystals. Specifically, it is found that the maximum out-of-plane piezoresponse is 0.56 pm V -1 , which is as strong as that observed in conventional 2D piezoelectric materials. The charges are found to be highly stable at room temperature with a trapping energy barrier of ≈2 eV.

36 MATERIALS SCIENCE↗