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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 OSTI2020

Rewiring the specificity of extracytoplasmic function sigma factors

Significance Bacterial phenotypes require the concerted expression of multiple genes, usually coordinated by a transcriptional regulator. Although the functions of many genes in sequenced bacterial genomes can be inferred, the regulatory networks that coordinate their expression are only known in a few model systems. Using a bioinformatic and experimental approach, we solve the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major class of bacterial regulators. We develop and use a high-stringency pipeline to predict the genes regulated by 67% of ECF σs in >10,000 species, providing a comprehensive look at the role of a broadly distributed family of gene regulatory proteins. This conceptual and computational framework is potentially applicable to other bacterial regulators.

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 OSTI2022

RIViT-seq enables systematic identification of regulons of transcriptional machineries

Abstract Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcription factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is laborious and not scalable. Here, we demonstrate regulon identification by in vitro transcription-sequencing (RIViT-seq) that enables systematic identification of regulons of transcription factors by combining an in vitro transcription assay and RNA-sequencing. Using this technology, target genes of 11 sigma factors were identified in Streptomyces coelicolor A3(2). The RIViT-seq data expands the transcriptional regulatory network in this bacterium, discovering regulatory cascades and crosstalk between sigma factors. Implementation of RIViT-seq with other transcription factors and in other organisms will improve our understanding of transcriptional regulatory networks across biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Transcription initiation as a control point in plastid gene expression

The extensive processing and protein-assisted stabilization of transcripts have been taken as evidence for a viewpoint that the control of gene expression had shifted entirely in evolution from transcriptional in the bacterial endosymbiont to posttranscriptional in the plastid. This suggestion is however at odds with many observations on plastid gene transcription. Chloroplasts of flowering plants and mosses contain two or more RNA polymerases with distinct promoter preference and division of labor for the coordinated synthesis of plastid RNAs. Plant and algal plastids further possess multiple nonredundant sigma factors that function as transcription initiation factors. The controlled accumulation of plastid sigma factors and modification of their activity by sigma-binding proteins and phosphorylation constitute additional transcriptional regulatory strategies. Plant and algal plastids also contain dedicated one- or two-component transcriptional regulators. Finally, transcription initiation thus continues to form a critical control point at which varied developmental and environmental signals intersect with plastid gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella

Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance and host-range is sparse. Here, we employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven diverse lytic phages including four new phages isolated from a therapeutic phage cocktail. We uncovered 301 diverse host factors essential in phage infection, many of which are shared between multiple phages demonstrating potential cross-resistance mechanisms. We validate many of these novel findings and uncover the intricate interplay between RpoS, the virulence-associated general stress response sigma factor and RpoN, the nitrogen starvation sigma factor in phage cross-resistance. Finally, the infectivity pattern of eleven phages across a panel of 23 genome sequenced Salmonella strains indicates that additional constraints and interactions beyond the host factors uncovered here define the phage host range.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Aerobic Respiration and Its Regulation in the Metal Reducer Shewanella oneidensis

Shewanella oneidensis MR-1 is a facultative anaerobe known for its ability to reduce metal oxides. Anaerobic respiration, especially metal reduction, has been the subject of extensive research. In contrast, S. oneidensis aerobic respiration has received less attention. S. oneidensis expresses cbb3- and aa3-type cytochrome c oxidases and a bd-type quinol oxidase. The aa3-type oxidase, which in other bacteria is the major oxygen reductase under oxygen replete conditions, does not appear to contribute to aerobic respiration and growth in S. oneidensis. Our results indicated that although the aa3-type oxidase does not play a role in aerobic growth on lactate, the preferred carbon source for S. oneidensis, it is involved in growth on pyruvate or acetate. These results highlight the importance of testing multiple carbon and energy sources when attempting to identify enzyme activities and mutant phenotypes. Several regulatory proteins contribute to the regulation of aerobic growth in S. oneidensis including CRP and ArcA. The 3',5'-cAMP phosphodiesterase (CpdA) appears to play a more significant role in aerobic growth than either CRP or ArcA, yet the deficiency does not appear to be the result of reduced oxidase genes expression. Interestingly, the ΔcpdA mutant was more deficient in aerobic respiration with several carbon sources tested compared to Δcrp, which was moderately deficient only in the presence of lactate. To identify the reason for ΔcpdA aerobic growth deficiency, we isolated a suppressor mutant with transposon insertion in SO_3550. Inactivation of this gene, which encodes an anti-sigma factor, restored aerobic growth in the cpdA mutant to wild-type levels. Inactivation of SO_3550 in wild-type cells, however, did not affect aerobic growth. The S. oneidensis genome encodes two additional CRP-like proteins that we designated CrpB and CrpC. Mutants that lack crpB and crpC were deficient in aerobic growth, but this deficiency was not due to the loss of oxidase gene expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) WhiB3 is an iron–sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σ A 4 ) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σ A 4 to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:σ A 4 complex without and with DNA at 1.5 Å and 2.45 Å, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:σ A 4 complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA-binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis. Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with σ A 4 and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Steam explosion pretreatment coupling high-temperature short-time sterilization facilitating cellulose degradation and sporulation-regulatory gene expression in high-solid fermentation

Steam explosion coupling high-temperature short-time sterilization (SE-HTST) was exploited to modify cellulosic biomass medium properties and promote high-solid fermentation (HSF). Biomass characterization analysis showed that SE-HTST enlarged microstructural pores and cavities in solid media, providing more effective space for microbial growth. Meanwhile, SE-HTST helped to release glucose from the cellulose with 35.8 ± 4.5, 20.0 ± 2.3, and 12.3 ± 5.7 mg glucose/g dry medium at 24, 48, and 72 h of fermentation, which were 3.1, 2.3, and 1.5 times higher than that in medium from conventional thermal sterilization (CTS), respectively. SE-HTST increased the viable cell and spore number of Bacillus subtilis by 1.8 and 1.6 times at 72 h of fermentation compared to CTS. Moreover, the expressions of master transcriptional gene spo0A and the early sigma factors of sigF and sigE genes gradually increased in the SE-HTST medium, showing enhanced sporulation in HSF. Therefore, SE-HTST is an effective strategy for facilitating cellulose degradation, improving glucose nutrients in biomass medium, and promoting sporulation-regulatory gene expression during high-solid fermentation, which enhances the production of microbial ecological agents using B. subtilis significantly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria

Abstract Transcription rates are regulated by the interactions between RNA polymerase, sigma factor, and promoter DNA sequences in bacteria. However, it remains unclear how non-canonical sequence motifs collectively control transcription rates. Here, we combine massively parallel assays, biophysics, and machine learning to develop a 346-parameter model that predicts site-specific transcription initiation rates for any σ 70 promoter sequence, validated across 22132 bacterial promoters with diverse sequences. We apply the model to predict genetic context effects, design σ 70 promoters with desired transcription rates, and identify undesired promoters inside engineered genetic systems. The model provides a biophysical basis for understanding gene regulation in natural genetic systems and precise transcriptional control for engineering synthetic genetic systems.

42 ENGINEERING↗
DOE OSTI2024

Mechanism of anion exchange and small-molecule inhibition of pendrin

Pendrin (SLC26A4) is an anion exchanger that mediates bicarbonate (HCO 3 - ) exchange for chloride (Cl-) and is crucial for maintaining pH and salt homeostasis in the kidney, lung, and cochlea. Pendrin also exports iodide (I - ) in the thyroid gland. Pendrin mutations in humans lead to Pendred syndrome, causing hearing loss and goiter. Inhibition of pendrin is a validated approach for attenuating airway hyperresponsiveness in asthma and for treating hypertension. However, the mechanism of anion exchange and its inhibition by drugs remains poorly understood. We applied cryo-electron microscopy to determine structures of pendrin from Sus scrofa in the presence of either Cl - , I - , HCO 3 - or in the apo-state. The structures reveal two anion-binding sites in each protomer, and functional analyses show both sites are involved in anion exchange. The structures also show interactions between the Sulfate Transporter and Anti-Sigma factor antagonist (STAS) and transmembrane domains, and mutational studies suggest a regulatory role. We also determine the structure of pendrin in a complex with niflumic acid (NFA), which uncovers a mechanism of inhibition by competing with anion binding and impeding the structural changes necessary for anion exchange. These results reveal directions for understanding the mechanisms of anion selectivity and exchange and their regulations by the STAS domain. This work also establishes a foundation for analyzing the pathophysiology of mutations associated with Pendred syndrome.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations

Abstract Mutations within the mtrR gene are commonly found amongst multidrug resistant clinical isolates of Neisseria gonorrhoeae, which has been labelled a superbug by the Centers for Disease Control and Prevention. These mutations appear to contribute to antibiotic resistance by interfering with the ability of MtrR to bind to and repress expression of its target genes, which include the mtrCDE multidrug efflux transporter genes and the rpoH oxidative stress response sigma factor gene. However, the DNA-recognition mechanism of MtrR and the consensus sequence within these operators to which MtrR binds has remained unknown. In this work, we report the crystal structures of MtrR bound to the mtrCDE and rpoH operators, which reveal a conserved, but degenerate, DNA consensus binding site 5′-MCRTRCRN4YGYAYGK-3′. We complement our structural data with a comprehensive mutational analysis of key MtrR-DNA contacts to reveal their importance for MtrR-DNA binding both in vitro and in vivo. Furthermore, we model and generate common clinical mutations of MtrR to provide plausible biochemical explanations for the contribution of these mutations to multidrug resistance in N. gonorrhoeae. Collectively, our findings unveil key biological mechanisms underlying the global stress responses of N. gonorrhoeae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Hard Synchrotron Spectra from Magnetically Dominated Plasma Turbulence

Synchrotron emission from astrophysical nonthermal sources usually assumes that the emitting particles are isotropic. By means of large-scale two- and three-dimensional particle-in-cell simulations, we demonstrate that the dissipation of magnetically dominated (${\sigma }_{0}\gg 1$) turbulence in pair plasmas leads to strongly anisotropic particle distributions. At Lorentz factors $\sim {\sigma }_{0}{\gamma }_{\mathrm{th}0}$ (here, ${\gamma }_{\mathrm{th}0}$ is the initial Lorentz factor), the particle velocity is preferentially aligned with the local magnetic field; instead, the highest energy particles are preferentially oriented in the plane perpendicular to the field. This energy-dependent anisotropy leads to a synchrotron spectral flux $\nu {F}_{\nu }\propto {\nu }^{s}$ that is much harder than for isotropic particles. Remarkably, for ${\sigma }_{0}\gg 1$ we find that the angle-integrated spectral slope in the slow cooling regime is $s\sim 0.5-0.7$ for a wide range of turbulence fluctuations, $0.25\lesssim \delta {B}_{\mathrm{rms}0}^{2}/{B}_{0}^{2}\lesssim 4$, despite significant variations in the power-law energy spectrum of nonthermal particles. This is because weaker turbulence levels imprint a stronger degree of anisotropy, thereby counteracting the effect of the steeper particle spectrum. The synchrotron spectral slope may be even harder, $s\gtrsim 0.7$, if the observer is in the plane perpendicular to the mean magnetic field. Our results are independent of domain size and dimensionality. Further, our findings may help explain the origin of hard synchrotron spectra of astrophysical nonthermal sources, most notably the radio spectrum of pulsar wind nebulae.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Nucleon form factors and the pion-nucleon sigma term

This talk summarizes the progress made since Lattice 2021 in understanding and controlling the contributions of towers of multihadron excited states with mass gaps starting lower than of radial excitations, and in increasing our confidence in the extraction of ground state nucleon matrix elements. The most clear evidence for multihadron excited state contributions (ESC) is in axial/pseudoscalar form factors that are required to satisfy the PCAC relation between them. The talk examines the broader question--which and how many of the theoretically allowed positive parity states N(p)π(−p), N(0)π(0)π(0), N(p)π(0), N(0)π(p), … make significant contributions to a given matrix element? New data for the axial, electric and magnetic form factors are presented. They continue to show trends observed in Ref.[1]. The N2LO χPT analysis of the ESC to the pion-nucleon sigma term, σπN, has been extended to include the Δ as an explicit degree of freedom [2]. The conclusion reached in Ref.[3] that Nπ and Nππ states each contribute about 10 MeV to σπN, and the consistency between the lattice result with Nπ state included and the phenomenological estimate is not changed with this improvement.

Gupta, Rajan↗
DOE OSTI2024

Measurement of Born cross section of $$ {e}^{+}{e}^{-}\to {\Sigma}^{+}{\overline{\Sigma}}^{-} $$ at center-of-mass energies between 3.510 and 4.951 GeV

Abstract Using 24.1 fb −1 ofe + e − collision data collected with the BESIII detector at the BEPCII collider, the Born cross sections and effective form factors of the$$ {e}^{+}{e}^{-}\to {\Sigma}^{+}{\overline{\Sigma}}^{-} $$ e + e − → Σ + Σ ¯ − reaction are measured. The measurements are performed at center-of-mass energies ranging from 3.510 to 4.951 GeV. No significant evidence for the decay of the charmonium(-like) states,ψ(3770),ψ(4040),ψ(4160),Y(4230),Y(4360),ψ(4415), andY(4660), into a$$ {\Sigma}^{+}{\overline{\Sigma}}^{-} $$ Σ + Σ ¯ − final state is observed. Consequently, upper limits for the products of the branching fractions and the electronic partial widths at the 90% confidence level are reported for these decays.

Physics↗
DOE OSTI2026

$\overline{\Sigma }^{\pm }$ production in $\text {pp}$ and $\text {p}{-}\text{Pb}$ collisions at $\sqrt{s_{\textrm{NN}}} = 5.02$ TeV with ALICE

The transverse momentum spectra and integrated yields of anti-$Σ$ hyperons ($\overline{\Sigma}^{\pm}$) have been measured in and collisions at $\sqrt{s_{\textrm{NN}}} = 5.02$ TeV with the ALICE experiment. Measurements are performed via the newly accessed decay channel $\overline{\Sigma}^{\pm}$ → $\bar{\textrm{n}}π^±$. A new method of antineutron reconstruction with the PHOS electromagnetic spectrometer is developed and applied to this analysis. The p T spectra of $\overline{\Sigma}^{\pm}$ are measured in the range 0.5 < p T < 3 GeV/c and compared to predictions of the PYTHIA 8, DPMJET, PHOJET, EPOS LHC and EPOS4 models. The EPOS LHC and EPOS4 models provide the best descriptions of the measured spectra both in pp and p-Pb collisions, while models which do not account for multiparton interactions provide a considerably worse description at high p T . The total yields of $\overline{\Sigma }^{\pm }$ in both pp and p-Pb collisions are compared to predictions of the Thermal-FIST model and dynamical models PYTHIA 8, DPMJET, PHOJET, EPOS LHC and EPOS4. All models reproduce the total yields in both colliding systems within uncertainties. The nuclear modification factors R pPb for both $\overline{\Sigma}^{+}$ and $\overline{\Sigma}^{-}$ are evaluated and compared to those of protons, $Λ$ and $Ξ$ hyperons, and predictions of EPOS LHC and EPOS4 models. No deviations of R pPb for $\overline{\Sigma}^{\pm}$ from the model predictions or measurements for other hadrons are found within uncertainties.

Abualrob, I. J. [University of Houston] (ORCID:000↗
DOE OSTI2023

Fast estimation of the look-elsewhere effect using Gaussian random fields

Abstract We discuss the use of Gaussian random fields to estimate the look-elsewhere effect correction. We show that Gaussian random fields can be used to model the null-hypothesis significance maps from a large set of statistical problems commonly encountered in physics, such as template matching and likelihood ratio tests. Some specific examples are searches for dark matter using pixel arrays, searches for astronomical transients, and searches for fast-radio bursts. Gaussian random fields can be sampled efficiently in the frequency domain, and the excursion probability can be fitted with these samples to extend any estimation of the look-elsewhere effect to lower p values. In addition, in cases where the Gaussian random field is stationary and the parameter space is Euclidean, the look-elsewhere effect correction can be computed analytically. We demonstrate these methods using two example template matching problems. Finally, we apply these methods to estimate the trial factor of a $$4^3$$ 4 3 accelerometer array for the detection of dark matter tracks in the Windchime project. When a global significance of $$3\sigma $$ 3 σ is required, the estimated trial factor for such an accelerometer array is $$10^{14}$$ 10 14 for a one-second search, and $$10^{22}$$ 10 22 for a 1-year search.

Qin, Juehang (ORCID:0000000182288949)↗
DOE OSTI2024

Cosmological Constraints from Combining Photometric Galaxy Surveys and Gravitational Wave Observatories

Spatial variations in survey properties due to selection effects generate substantial systematic errors in large-scale structure measurements in optical galaxy surveys on very large scales. On such scales, the statistical sensitivity of optical surveys is also limited by their finite sky coverage. By contrast, gravitational wave (GW) sources appear to be relatively free of these issues, provided the angular sensitivity of GW experiments can be accurately characterized. We quantify the expected cosmological information gain from combining the forecast LSST 3$\times$2pt analysis (combination of three 2-point correlations of galaxy density and weak lensing shear fields) with the large-scale auto-correlation of GW sources from proposed next-generation GW experiments. We find that in $\Lambda$CDM and $w$CDM models, there is no significant improvement in cosmological constraints from combining GW with LSST 3$\times$2pt over LSST alone, due to the large shot noise for the former; however, this combination does enable a $\sim6\%$ constraint on the linear galaxy bias of GW sources. More interestingly, the optical-GW data combination provides tight constraints on models with primordial non-Gaussianity (PNG), due to the predicted scale-dependent bias in PNG models on large scales. Assuming that the largest angular scales that LSST will probe are comparable to those in Stage III surveys ($\ell_{\rm min}\sim50$), the inclusion of next-generation GW measurements could improve constraints on the PNG parameter $f_{\rm NL}$ by up to a factor of $\simeq6.6$ compared to LSST alone, yielding $\sigma(f_{\rm NL})=8.5$. These results assume the expected capability of a network of Einstein Telescope-like GW observatories, with a detection rate of $10^6$ events/year. We investigate the sensitivity of our results to different assumptions about future GW detectors as well as different LSST analysis choices.

79 ASTRONOMY AND ASTROPHYSICS↗