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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Unexpected trends in the enhanced Ce 3+ surface concentration in ceria–zirconia catalyst materials

Despite the immense importance of ceria–zirconia solid solutions in heterogeneous catalysis, and the growing consensus that catalytic activity correlates with the concentration of reduced Ce 3+ species and accompanying oxygen vacancies, the extent of reduction at the surfaces of these materials, where catalysis occurs, is unknown. Using angle-resolved X-ray Absorption Near Edge Spectroscopy (XANES), we quantify under technologically relevant conditions the Ce 3+ concentration in the surface (2–3 nm) and bulk regions of ceria–zirconia films grown on single crystal yttria-stabilized zirconia, YSZ (001). In all circumstances, we observe substantial Ce 3+ enrichment at the surface relative to the bulk. Surprisingly, the degree of enhancement is highest in the absence of Zr. This behavior stands in direct contrast to that of the bulk in which the Ce 3+ concentration monotonically increases with increasing Zr content. Overall, these results suggest that while Zr enhances the oxygen storage capacity in ceria, undoped ceria may have higher surface catalytic activity. They further urge caution in the use of bulk properties as surrogate descriptors for surface characteristics and hence catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A General Binary Isotherm Model for Amines Interacting with CO 2 and H 2 O

CO 2 capture by primary or secondary amines has been of great research interests for a century because of its industrial importance. Interest has grown even more, because of the need to eliminate the CO 2 emissions that drive global warming. Experimental evidence shows that CO 2 sorption in primary or secondary amines is accompanied by co-absorption of H 2 O. A quantitative analysis of such CO 2 -H 2 O co-absorption behavior is important for practical process design and theoretical understanding. Even though there is almost an experimental consensus that water enhances CO 2 uptake capacity, an analytic model to explain this phenomenon is not well established. Instead, some empirical models such as the Toth model are used to describe the isotherm without accounting for the presence of water. Recently, we have demonstrated that the isotherm equation of CO 2 sorption into strong-base anion exchange materials with quaternary ammonium can be derived from that of strong-base aqueous alkaline solutions by correcting for the drastic change in water activity and by including an appropriate parameterization of the water activity terms. In this paper, we generalize this model from quaternary ammonium to primary, secondary and tertiary amines either in solutions or as functional groups in polymer resins. For primary, secondary and tertiary amines, the isotherm equation can be derived by extending that of a weak-base aqueous alkaline solution such as aqueous ammonia. The model has been validated using experimental data of aqueous ammonia in literature. Furthermore, this general model even includes quaternary ammonium as a special limit. Hence, this general model offers a platform that can treat the isotherms of solid amines, aqueous amines and aqueous alkaline solutions in a unified way.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Sequence-defined structural transitions by calcium-responsive proteins

Biopolymer sequences dictate their functions, and protein-based polymers are a promising platform to establish sequence–function relationships for novel biopolymers. To efficiently explore vast sequence spaces of natural proteins, sequence repetition is a common strategy to tune and amplify specific functions. This strategy is applied to repeats-in-toxin (RTX) proteins with calcium-responsive folding behavior, which stems from tandem repeats of the nonapeptide GGXGXDXUX in which X can be any amino acid and U is a hydrophobic amino acid. To determine the functional range of this nonapeptide, we modified a naturally occurring RTX protein that forms β-roll structures in the presence of calcium. Sequence modifications focused on calcium-binding turns within the repetitive region, including either global substitution of nonconserved residues or complete replacement with tandem repeats of a consensus nonapeptide GGAGXDTLY. Some sequence modifications disrupted the typical transition from intrinsically disordered random coils to folded β rolls, despite conservation of the underlying nonapeptide sequence. Proteins enriched with smaller, hydrophobic amino acids adopted secondary structures in the absence of calcium and underwent structural rearrangements in calcium-rich environments. In contrast, proteins with bulkier, hydrophilic amino acids maintained intrinsic disorder in the absence of calcium. In conclusion, these results indicate a significant role of nonconserved amino acids in calcium-responsive folding, thereby revealing a strategy to leverage sequences in the design of tunable, calcium-responsive biopolymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Modeling active nematics via the nematic locking principle

Active nematic systems consist of rod-like internally driven subunits that interact with one another to form large-scale coherent flows. They are important examples of far-from-equilibrium fluids, which exhibit a wealth of nonlinear behavior. This includes active turbulence, in which topological defects in the nematic order braid around one another in a chaotic fashion. One of the most studied examples of active nematics consists of a dense two-dimensional layer of microtubules, crosslinked by kinesin molecular motors that inject extensile deformations into the fluid. Though numerous theoretical studies have modeled microtubule-based active nematics, no consensus has emerged on how to fully and quantitatively capture the features of the experimental system. Here, to better understand the theoretical foundations for modeling this system, we propose a fundamental principle we call the nematic locking principle—individual microtubules cannot rotate without all neighboring microtubules also rotating. Physically, this is justified by the high density of the microtubules, their elongated nature, and their corresponding steric interactions. We assert that the nematic locking principle holds throughout the majority of the material, but breaks down in the neighborhood of topological defects and other regions of low density. We derive the most general nematic transport equation consistent with this principle and also derive the most general term that violates it, introducing fracturing into the material. We then examine the standard Beris–Edwards approach, commonly used to model this system, and show that it violates the nematic locking principle throughout the majority of the material due to fracturing. We then propose a modification to the Beris–Edwards model that enforces nematic locking nearly everywhere. This modification shuts off fracturing except in regions where the order parameter (a proxy for density) is reduced. In these regions fracturing is turned on. The resulting simulations in turn show strong nematic locking throughout the bulk of the material, with narrow bands of fracturing, consistent with experimental observation. One additional advantage of enforcing nematic locking is that nontrivial stationary state solutions, common in Beris–Edwards simulations but not seen in experiments, are eliminated.

Mitchell, Kevin A. [Univ. of California, Merced, C↗
DOE OSTI2020

Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa

Infective endocarditis (IE) is a cardiovascular disease often caused by bacteria of the viridans group of streptococci, which includes Streptococcus gordonii and Streptococcus sanguinis. Previous research has found that serine-rich repeat (SRR) proteins on the S. gordonii bacterial surface play a critical role in pathogenesis by facilitating bacterial attachment to sialylated glycans displayed on human platelets. Despite their important role in disease progression, there are currently no anti-adhesive drugs available on the market. Here, we performed structure-based virtual screening using an ensemble docking approach followed by consensus scoring to identify novel small molecule effectors against the sialoglycan binding domain of the SRR adhesin protein Hsa from the S. gordonii strain DL1. The screening successfully predicted nine compounds which were able to displace the native ligand (sialyl-T antigen) in an in vitro assay and bind competitively to Hsa. Furthermore, hierarchical clustering based on the MACCS fingerprints showed that eight of these small molecules do not share a common scaffold with the native ligand. This study indicates that SRR family of adhesin proteins can be inhibited by diverse small molecules and thus prevent the interaction of the protein with the sialoglycans. This opens new avenues for discovering potential drugs against IE.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

The DESI DR1 peculiar velocity survey: Growth rate measurements from the galaxy power spectrum

The large-scale structure of the Universe and its evolution encapsulate a wealth of cosmological information. A powerful means of unlocking this knowledge lies in measuring the auto-power spectrum and/or the cross-power spectrum of the galaxy density and momentum fields, followed by the estimation of cosmological parameters based on these spectrum measurements. In this study, we generalize the cross-power spectrum model to accommodate scenarios in which the density and momentum fields are derived from distinct galaxy surveys. The growth rate of the large-scale structures of the Universe, commonly represented as fσ 8 , was extracted by jointly fitting the monopole and quadrupole moments of the auto-density power spectrum, the monopole of the auto-momentum power spectrum, and the dipole of the cross-power spectrum. Our estimators, theoretical models, and parameter-fitting framework were tested using mocks, confirming their robustness and accuracy in retrieving the fiducial growth rate from simulation. These techniques were then applied to analyse the power spectrum of the DESI Bright Galaxy Survey and Peculiar Velocity Survey. The fit result of the growth rate is fσ8 = 0.440$^{+0.080}_{−0.096}$ at effective redshift zeff = 0.07. By synthesizing the fitting outcomes from correlation functions, maximum likelihood estimation, and the power spectrum, a consensus value is yielded of fσ 8 (z eff = 0.07) = 0.450$^{+0.055}_{−0.055}$, and correspondingly we obtain γ = 0.580$^{+0.110}_{−0.110}$, Ω m = 0.301$^{+0.011}_{−0.011}$, and σ 8 = 0.834$^{+0.032}_{−0.032}$. The measured fσ8 and γ are consistent with the prediction of the Λ cold dark matter model and general relativity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

The gas-phase mass–metallicity relation of dwarf galaxies across large-scale environments using the CAVITY parent sample

Context. The gas-phase mass–metallicity relation (MZR) of galaxies shows a noticeable break in slope and an increased scatter at low stellar masses, suggesting that the physical processes governing chemical enrichment differ between dwarf and high-mass systems. Dwarf galaxies, in particular, are highly susceptible to both internal and environmental mechanisms due to their shallow potential wells. Aims. The primary aim of this work is to assess whether a single, universal MZR can describe dwarf galaxies across diverse large-scale environments, or whether systematic environmental variations emerge. To probe these, we examine the MZR and star formation rate (SFR) of dwarf galaxies with stellar masses in the range of 8.9 < log(M ★ /M ⊙ ) < 9.5. Methods. Using optical spectra from the Sloan Digital Sky Survey, we measured the fluxes of key emission lines via the pyPipe3D full spectral fitting pipeline. Aperture-corrected fluxes, along with multiple metallicity indicators and calibrations, were used to derive the MZR and the SFR for 353, 311, and 22 dwarf galaxies located in voids, filaments, and clusters, respectively. Results. We find a systematic variation in the MZR slope, steeper in voids (0.28 ± 0.03) and progressively flatter in clusters (0.17 ± 0.08), indicating a dependence of the MZR on the large-scale environment in this mass regime. When galaxies are separated by local density, no significant differences are observed between isolated and non-isolated dwarfs in voids. Isolated dwarf galaxies in filaments also exhibit properties similar to those of their counterparts in voids. However, non-isolated filament galaxies exhibit similar MZR slopes comparable to those of cluster dwarfs and flatter slopes than their counterparts in voids. Conclusions. We report both large- and local-scale environmental dependencies in the gas-phase metallicity and in the slope of the MZR for dwarf galaxies. Consistent with the general consensus on the pre-processing of galaxies in filaments, our results indicate that the influence of the local environment becomes increasingly significant within the filamentary regions of the cosmic web, affecting the chemical enrichment and star formation activity of low-mass systems. These findings further suggest that a portion of the scatter commonly observed in the MZR of dwarf galaxies arises from environmental effects.

Bidaran, Bahar [Dpto. de Física Teórica y del Cosm↗
DOE OSTI2024

An introduction to Spent Nuclear Fuel decay heat for Light Water Reactors: a review from the NEA WPNCS

This paper summarized the efforts performed to understand decay heat estimation from existing spent nuclear fuel (SNF), under the auspices of the Working Party on Nuclear Criticality Safety (WPNCS) of the OECD Nuclear Energy Agency. Needs for precise estimations are related to safety, cost, and optimization of SNF handling, storage, and repository. The physical origins of decay heat (a more correct denomination would be decay power) are then introduced, to identify its main contributors (fission products and actinides) and time-dependent evolution. Due to limited absolute prediction capabilities, experimental information is crucial; measurement facilities and methods are then presented, highlighting both their relevance and our need for maintaining the unique current full-scale facility and developing new ones. The third part of this report is dedicated to the computational aspect of the decay heat estimation: calculation methods, codes, and validation. Different approaches and implementations currently exist for these three aspects, directly impacting our capabilities to predict decay heat and to inform decision-makers. Finally, recommendations from the expert community are proposed, potentially guiding future experimental and computational developments. One of the most important outcomes of this work is the consensus among participants on the need to reduce biases and uncertainties for the estimated SNF decay heat. If it is agreed that uncertainties (being one standard deviation) are on average small (less than a few percent), they still substantially impact various applications when one needs to consider up to three standard deviations, thus covering more than 95% of cases. The second main finding is the need of new decay heat measurements and validation for cases corresponding to more modern fuel characteristics: higher initial enrichment, higher average burnup, as well as shorter and longer cooling time. Similar needs exist for fuel types without public experimental data, such as MOX, VVER, or CANDU fuels. A third outcome is related to SNF assemblies for which no direct validation can be performed, representing the vast majority of cases (due to the large number of SNF assemblies currently stored, or too short or too long cooling periods of interest). A few solutions are possible, depending on the application. For the final repository, systematic measurements of quantities related to decay heat can be performed, such as neutron or gamma emission. This would provide indications of the SNF decay heat at the time of encapsulation. For other applications (short- or long-term cooling), the community would benefit from applying consistent and accepted recommendations on calculation methods, for both decay heat and uncertainties. This would improve the understanding of the results and make comparisons easier.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Normative Ranges for Oculomotor and Reaction Time Tests in U.S. Military Service Members and Veterans

AbstractBackground Oculomotor and reaction time tests are frequently used assessments of vestibular symptoms, traumatic brain injury (TBI), or other neurological disorders in both clinical and research contexts. When interpreting these tests it is important to have a reference interval (RI) as a comparison for what constitutes a typical/expected response; however, the current body of research has only limited information regarding normative ranges calculated according to established standards or for a military-specific sample.Purpose The purpose of the present study was to describe RIs for oculomotor and reaction time tests in a cohort of service members and veterans (SMVs) for use as comparators by clinicians and scientists.Research Design Descriptive.Study Sample Participants were prospectively enrolled in the Defense and Veterans Brain Injury Center-Traumatic Brain Injury Center of Excellence 15-year Longitudinal Traumatic Brain Injury Study. Only SMVs without a history of TBI or blast exposure were included in the RI calculations.Data Collection and Analysis The test paradigms included in this analysis were: smooth pursuit, prosaccades, antisaccades, saccades and reaction time, predictive saccades, optokinetic nystagmus, auditory reaction time, and visual reaction time. Nonparametric methods, based on the U.S. Food and Drug Administration's recognized consensus standards, were used to calculate 95% RIs. A comparison between the calculated RIs and those available from previously published research is provided.Results Summary statistics and RIs were calculated for 47 outcome parameters from 13 oculomotor and reaction time tests. Sample sizes and age ranges varied across outcome parameters depending on the availability of reference values for RI calculations. The sample sizes used to calculate RIs ranged from 51 to 69. The age of SMVs included in each RI ranged from 19 to 61 years with mean ages ranging from 37 to 39 years. Similarities/differences between the RIs in the present study and those in previously published research are highly dependent on the outcome parameter; however, in general, the RIs in the present study tended to be somewhat wider.Conclusion The RIs provided in this paper can serve as comparisons for clinicians and scientists who are utilizing these oculomotor and reaction time testing paradigms in similar cohorts of patients or research participants.

Audiology & Speech-Language Pathology↗
DOE OSTI2021

Time to Use Dendrohydrological Data in Water Resources Management?

Despite a wide consensus on the potential importance of streamflow reconstructions to water resources planning and management activities, applications of dendrohydrology have been piecemeal. This review article describes barriers to widespread use of dendrohydrological data and suggests research needs for operationalizing streamflow records reconstructed from these proxy data.

42 ENGINEERING↗
DOE OSTI2024

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein

Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Re-examining the silicon self-interstitial charge states and defect levels: A density functional theory and bounds analysis study

The self-interstitial atom (SIA) is one of two fundamental point defects in bulk Si. Isolated Si SIAs are extremely difficult to observe experimentally. Even at very low temperatures, they anneal before typical experiments can be performed. Given the challenges associated with experimental characterization, accurate theoretical calculations provide valuable information necessary to elucidate the properties of these defects. Previous studies have applied Kohn–Sham density functional theory (DFT) to the Si SIA, using either the local density approximation or the generalized gradient approximation to the exchange-correlation (XC) energy. The consensus of these studies indicates that a Si SIA may exist in five charge states ranging from -2 to +2 with the defect structure being dependent on the charge state. This study aims to re-examine the existence of these charge states in light of recently derived “approximate bounds” on the defect levels obtained from finite-size supercell calculations and new DFT calculations using both semi-local and hybrid XC approximations. We conclude that only the neutral and +2 charge states are directly supported by DFT as localized charge states of the Si SIA. Within the current accuracy of DFT, our results indicate that the +1 charge state likely consists of an electron in a conduction-band-like state that is coulombically bound to a +2 SIA. Furthermore, the -1 and -2 charge states likely consist of a neutral SIA with one and two additional electrons in the conduction band, respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Bulk dissipation in the quantum anomalous Hall effect

Even at the lowest accessible temperatures, measurements of the quantum anomalous Hall (QAH) effect have indicated the presence of parasitic dissipative conduction channels. There is no consensus whether parasitic conduction is related to processes in the bulk or along the edges. Here, we approach this problem by comparing transport measurements of Hall bar and Corbino geometry devices fabricated from Cr-doped (BiSb) 2 Te 3 . We identify bulk conduction as the dominant source of dissipation at all values of temperature and in-plane electric field. Furthermore, we observe identical breakdown phenomenology in both geometries, indicating that breakdown of the QAH phase is a bulk process. The methodology developed in this study could be used to identify dissipative conduction mechanisms in new QAH materials, ultimately guiding material development towards realization of the QAH effect at higher temperatures

36 MATERIALS SCIENCE↗
DOE OSTI2022

Enforcing detailed balance in the Borgnakke–Larsen redistribution method with temperature dependent relaxation models

For decades, it has been observed that the commonly used Borgnakke–Larsen method for energy redistribution in Direct Simulation Monte Carlo codes fails to satisfy the principle of detailed balance when coupled to a wide variety of temperature dependent relaxation models, while seemingly satisfying detailed balance when coupled to others. Many attempts have been made to remedy the issue, yet much ambiguity remains, and no consensus appears in the literature regarding the root cause of the intermittent compatibility of the Borgnakke–Larsen method with temperature dependent relaxation models. This paper alleviates that ambiguity by presenting a rigorous theoretical derivation of the Borgnakke–Larsen method's requirement for satisfying detailed balance. Specifically, it is shown that the Borgnakke–Larsen method maintains detailed balance if and only if the probability of internal-energy exchange during a collision depends only on collision invariants (e.g., total energy). Here, the consequences of this result are explored in the context of several published definitions of relaxation temperature, including translational, total, and cell-averaged temperatures. Of particular note, it is shown that cell-averaged temperatures, which have been widely discussed in the literature as a way to ensure equilibrium is reached, also fail in a similar, although less dramatic, fashion when the aforementioned relationship is not enforced. The developed theory can be used when implementing existing or new relaxation models and will ensure that detailed balance is satisfied.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

A review on charged-particle transport modeling for laser direct-drive fusion

Inertial confinement fusion (ICF) with the laser-indirect-drive scheme has recently made a tremendous breakthrough recently after decades of intensive research effort. Taking this success to the next step, the ICF community is coming to a general consensus that laser direct-drive (LDD) fusion might be the viable way for enabling inertial fusion energy (IFE) and high-gain targets for other applications. Designing and understanding LDD fusion targets heavily rely on radiation-hydrodynamic code simulations, in which charged-particle transport plays an essential role in modeling laser-target energy coupling and bootstrap heating of fusion-produced α-particles. To better simulate charged-particle transport in LDD targets, over the past four decades the plasma physics community has advanced transport calculations from simple plasma physics models to sophisticated computations based on first-principles methods. In this review, we give an overview of the current status of charged-particle transport modeling for LDD fusion, including what challenges we still face and the possible paths moving forward to advance transport modeling for ICF simulations. We hope this review will provide a summary of exciting challenges to stimulate young minds to enter the field, facilitate further progress in understanding warm-dense matter physics, and ultimately bridge toward the success of reliable LDD fusion designs for IFE and other high-gain ICF applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Effects of stoichiometry and epitaxial strain on the stabilization of infinite-layer nickelates

The discovery of superconductivity in infinite-layer nickelates has sparked great interest due to their potential analogy with the unconventional cuprate superconductors. However, investigations of this system have been limited by the challenges in materials control and synthesis driven by substantial thermodynamic instability, making it difficult to reach an experimental consensus. Hence, establishing a robust synthetic route to highly crystalline infinite-layer nickelates is of paramount importance. Here, we present and discuss recent progress on the reproducible two-step synthesis of (Nd,Sr)NiO2 via the stabilization of high-quality perovskite nickelates and the subsequent topotactic transition to the infinite-layer phase. In particular, we discuss the important factors, such as cation stoichiometry and epitaxial strain, which significantly impact the crystallinity of both phases, accompanied by careful structural characterization. These results on robust synthesis can help accelerate the experimental investigation of the intrinsic physical properties of these complex strongly correlated materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗
DOE OSTI2020

A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation

Using an in vitro transcription system with purified RNA polymerase (RNAP) to investigate rRNA synthesis in the photoheterotrophic α-proteobacterium Rhodobacter sphaeroides, we identified a surprising feature of promoters recognized by the major holoenzyme. Transcription from R. sphaeroides rRNA promoters was unexpectedly weak, correlating with absence of 7T, the very highly conserved thymine found at the last position in –10 elements of promoters in most bacterial species. Thymine substitutions for adenine at position –7 in the three rRNA promoters strongly increased intrinsic promoter activity, indicating that R. sphaeroides RNAP can utilize –7T when present. rRNA promoters were activated by purified R. sphaeroides CarD, a transcription factor found in many bacterial species but not in β- and γ-proteobacteria. Overall, CarD increased the activity of 15 of 16 native R. sphaeroides promoters tested in vitro that lacked –7T, whereas it had no effect on three of the four native promoters that contained –7T. Genome-wide bioinformatic analysis of promoters from R. sphaeroides and two other α-proteobacterial species indicated that 30 to 43% contained –7T, whereas 90 to 99% of promoters from non–α-proteobacteria contained –7T. Thus, promoters lacking –7T appear to be widespread in α-proteobacteria and may have evolved away from consensus to enable their coordinated regulation by transcription factors like CarD. We observed a strong reduction in R. sphaeroides CarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.

59 BASIC BIOLOGICAL SCIENCES↗