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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs

RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are frequently selected. However, we lack a systems view of how mutations alter the RNAP molecular functions to promote adaptation. We, therefore, measured the fitness of thousands of mutations within a region of rpoB under multiple conditions and genetic backgrounds, to find that adaptive mutations cluster in two modules. Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. Mutations in the other favor maintenance over growth through a destabilized RNAP-DNA complex. The two molecular handles capture the versatile RNAP-mediated adaptations. Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1973

Numerical simulation of small-scale thermal convection in the atmosphere

A Boussinesq system is integrated numerically in three dimensions and time in a study of nonhydrostatic convection in the atmosphere. Simulation of cloud convection is achieved by the inclusion of parametrized effects of latent heat and small-scale turbulence. The results are compared with the cell structure observed in Rayleigh-Benard laboratory conversion experiments in air. At a Rayleigh number of 4000, the numerical model adequately simulates the experimentally observed evolution, including some prominent transients of a flow from a randomly perturbed initial conductive state into the final state of steady large-amplitude two-dimensional rolls. At Rayleigh number 9000, the model reproduces the experimentally observed unsteady equilibrium of vertically coherent oscillatory waves superimposed on rolls.

Somerville, R. C. J.↗
DOE OSTI2019

Contribution of chiral three-body forces to the monopole component of the effective shell-model Hamiltonian

We present a study of the role played by realistic three-body forces in providing a reliable monopole component of the effective shell-model Hamiltonian. To this end, starting from a nuclear potential built up within the chiral perturbation theory, we derive effective shell-model Hamiltonians with and without the contribution of the three-body potential and compare the results of shell-model calculations with a set of observables that evidence shell-evolution properties. The testing ground of our investigation is nuclei belonging to the fp shell, since the shell-evolution towards shell closures in 48 Ca and 56 Ni provides a paradigm for shell-model Hamiltonians. Furthermore, our analysis shows that only by including contributions of the three-body force is the monopole component of the effective shell-model Hamiltonian then able to reproduce the experimental shell evolution towards and beyond the closure at N = 28.

39 ≤ A ≤ 58↗
DOE OSTI2021

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient

Significance Increasing evidence suggests that evolutionary processes frequently shape ecological patterns; however, most microbiome studies thus far have focused on only the ecological responses of these communities. By using parallel field experiments and focusing in on a model soil bacterium, we showed that bacterial “species” are differentially adapted to local climates, leading to changes in their composition. Furthermore, we detected strain-level evolution, providing direct evidence that both ecological and evolutionary processes operate on annual timescales. The consideration of eco-evolutionary dynamics may therefore be important to understand the response of soil microbiomes to future environmental change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Extending evolutionary forecasts across bacterial species

Improving evolutionary forecasting requires progressing from studying repeated evolution of a single genotype under identical conditions to formulating broad principles. These principles should enable predictions of how similar species will adapt to similar selective pressures. Evolve-and-resequence experiments with multiple species allow testing forecasts on different biological levels and elucidating the causes for failed predictions. Here, we show that forecasts for adaptation to static culture conditions can be extended to multiple species by testing previous predictions for Pseudomonas syringae and Pseudomonas savastanoi. In addition to sequence divergence, these species differ in their repertoire of biofilm regulatory genes and structural components. Consistent with predictions, both species repeatedly produced biofilm mutants with a wrinkly spreader phenotype. Predominantly, mutations occurred in the wsp operon, with less frequent promoter mutations near uncharacterized diguanylate cyclases. However, mutational patterns differed on the gene level, which was explained by a lack of conservation in relative fitness of mutants between more divergent species. The same mutation was the most frequent for both species suggesting that conserved mutation hotspots can increase parallel evolution. This study shows that evolutionary forecasts can be extended across species, but that differences in the genotype–phenotype–fitness map and mutational biases limit predictability on a detailed molecular level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Adaptive Laboratory Evolution for algal strain improvement: methodologies and applications

Originally developed in bacterial and fungal models, Adaptive Laboratory Evolution (ALE) experimentally selects for targeted phenotypes by allowing cells containing beneficial random genetic mutations to replicate more quickly in the presence of environmental stress. When applied to microalgae, this technique has been used to increase growth rate, stress tolerance, substrate utilization, and product yield. This review discusses ALE experimental design parameters, and summarizes key results and lessons learned from recent microalgal ALE studies. By documenting the current state of the field, we provide insight on the ways microalgal ALE might be used to develop commercially viable biotechnology strains.

09 BIOMASS FUELS↗
DOE OSTI2022

In vivo hypermutation and continuous evolution

Directed evolution has revolutionized biomolecular engineering by applying cycles of mutation, amplification and selection to genes of interest (GOIs). However, classical directed evolution methods that rely on manually staged evolutionary cycles constrain the scale and depth of the evolutionary search that is possible. Here we describe genetic systems that achieve cycles of rapid mutation, amplification and selection fully inside living cells, enabling the continuous evolution of GOIs as cells grow. These systems advance the scale, evolutionary search depth, ease and overall power of directed evolution and access important new areas of protein evolution and engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Temperature-dependent stability of θ'-Al 2 Cu precipitates investigated with phase field simulations and experiments

The upper limit of service temperature for many Al-Cu alloys is determined by the thermal stability of strengthening θ' (Al 2 Cu) precipitates. Above a certain temperature, θ' precipitates will undergo morphological evolution and transform into the detrimental, equilibrium θ phase, leading to a rapid drop in strength. Certain alloying elements have recently been reported to increase the thermal stability of θ' precipitates, by mechanisms that are yet unclear. Herein, we investigate the effect of modified interfacial energy and solute chemical mobility on the thermal stability of θ' via high-throughput phase field study. We identify a critical θ' aspect ratio to predict the onset of θ formation. Using this criterion, we predict the time required for θ' to θ phase transformation as a function of temperature, Cu diffusivity, and the interfacial energy of θ' precipitates. The predicted times compare favorably with reported times for θ formation under similar experimental conditions. Furthermore, these phase field simulations predict that a moderate reduction in Cu mobilityis adequate to stabilize the as-aged microstructure up to 300 °C, while substantial reductions to both interfacial energy and Cu mobility are needed to achieve similar stability at 400 °C. Experimental microstructural evolution results in commercial (319) and thermally stabilized (RR350) cast aluminum alloys are presented to complement the simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2019

High-resolution lineage tracking reveals travelling wave of adaptation in laboratory yeast

In rapidly adapting asexual populations, including many microbial pathogens and viruses, numerous mutant lineages often compete for dominance within the population. These complex evolutionary dynamics determine the outcomes of adaptation, but have been difficult to observe directly. Previous studies have used whole-genome sequencing to follow molecular adaptation; however, these methods have limited resolution in microbial populations. Here we introduce a renewable barcoding system to observe evolutionary dynamics at high resolution in laboratory budding yeast. We find nested patterns of interference and hitchhiking even at low frequencies. These events are driven by the continuous appearance of new mutations that modify the fates of existing lineages before they reach substantial frequencies. We observe how the distribution of fitness within the population changes over time, and find a travelling wave of adaptation that has been predicted by theory. We show that clonal competition creates a dynamical ‘rich-get-richer’ effect: fitness advantages that are acquired early in evolution drive clonal expansions, which increase the chances of acquiring future mutations. However, less-fit lineages also routinely leapfrog over strains of higher fitness. Finally, our results demonstrate that this combination of factors, which is not accounted for in existing models of evolutionary dynamics, is critical in determining the rate, predictability and molecular basis of adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantifying the local adaptive landscape of a nascent bacterial community

Abstract The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes (“L” and “S”) shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE). We engineered genome-wide barcoded transposon libraries to measure the invasion fitness effects of all possible gene knockouts in the coexisting strains as well as their ancestor, for many different, ecologically relevant conditions. We find consistent statistical patterns of fitness effect variation across both genetic background and community composition, despite the idiosyncratic behavior of individual knockouts. Additionally, fitness effects are correlated with evolutionary outcomes for a number of conditions, possibly revealing shifting patterns of adaptation. Together, our results reveal how ecological and epistatic effects combine to shape the adaptive landscape in a nascent ecological community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fermentation Practices Select for Thermostable Endolysins in Phages

Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into how environmental factors and ecological niches may have influenced the evolution of these enzymes. In this study, we focused on phages infecting Streptococcus thermophilus, as this bacterial species has a well-defined and narrow ecological niche, namely, dairy fermentation. Among the endolysins found in phages targeting this species, we observed limited diversity, with a singular structural type dominating in most of identified S. thermophilus phages. Within this prevailing endolysin type, we discovered a novel and highly conserved calcium-binding motif. This motif proved to be crucial for the stability and activity of the enzyme at elevated temperatures. Ultimately, we demonstrated its positive selection within the host's environmental conditions, particularly under the temperature profiles encountered in the production of yogurt, mozzarella, and hard cheeses that rely on S. thermophilus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microstructure Clones

Background: A material’s microstructure drives its material performance. Contemporary crystal plasticity experiments compare full-field strain measurements of polycrystal specimens to models. Because each specimen is unique, it is impossible to know which features of the observed deformation are deterministic vs statistical; thus, differences between model and experiment may or may not be significant. Objective: This paper introduces the invention of microstructure clones. Microstructure clones are 2D oligocrystal specimens that have nearly identical microstructures to remedy the aforementioned experimental limitations. Having specimens with nearly identical microstructures will allow for multiple destructive tests of a microstructure (either as repeats or intentionally different experiments), an ability to “see the future” by providing insight into how a specimen will deform, variability quantification, and experimental investigations of response to small microstructural changes. Methods: This work introduces microstructure clones. Repeatability of these clones is demonstrated in tensile bars of pure nickel. Local strain measurements from digital image correlation are compared between clone specimens and compared to results from a crystal plasticity finite element model. Results: Two sets of microstructure clones were tested in this study and displayed very consistent deformation responses within each clone set. Small observed differences in deformation invite investigation into microstructure stochasticity and the effect of small microstructural and loading differences. Conclusions: Microstructure clones represent a significant shift in understanding structure–property relationships. This work reshapes experimental crystal plasticity to allow for experiments that control for specific variables, quantification of microstructural stochasticity (and other sources of stochasticity), and opportunities for replicating experiments.

Crystal Plasticity↗
DOE OSTI2024

Computational analysis of flame initiation, quenching, and re-ignition in a prechamber natural gas engine under varying EGR-dilution levels

The on-road natural-gas (NG) fueled transportation relies on stoichiometric spark-ignition engines for the advantages of simple after-treatment system despite the efficiency penalty relative to lean-burn combustion strategies. Exhaust gas recirculation (EGR) has the potential to reduce this efficiency gap at low to moderate loads without the need for complex lean-exhaust aftertreatment systems. However, EGR dilution leads to reduced combustion stability and increased cycle-to-cycle variability. A promising technology that has the potential to achieve reliable operation under diluted conditions is the prechamber ignition (or turbulent jet ignition) which uses chemically active turbulent jets generated from combustion inside a prechamber to initiate, stabilize and accelerate combustion of the mixture inside the main chamber. The present work focusses on developing a RANS-based CFD approach to accurately reproduce in-cylinder phenomena in a stoichiometric NG prechamber-assisted heavy-duty engine without relying on complex combustion models that account for turbulence-chemistry interactions. This is necessary because reactive prechamber jets at high EGR dilution tend to extinguish while emerging into the main chamber, which is followed by a phase of re-ignition — a phenomenon that conventional G-equation or well-stirred reactor combustion models cannot reproduce. With addition of a damping multiplier to the well-stirred reactor model, the predictions are seen to show good agreement with experimental pressure evolution and combustion images acquired from a single cylinder Cummins N-14 optical diesel engine retrofitted with a prechamber ignition system. Model predictions of local heat release in the flame and temperature evolution inside the flame are used to investigate combustion dynamics in the prechamber and the main chamber. It is seen that the well-stirred reactor model with the inclusion of damping is able to reproduce the temporary reduction in heat release within the flame, which can be considered equivalent to quenching of jets, and the subsequent re-ignition of the flame inside the main chamber. The delay between quenching and re-ignition depends on the amount of dilution, as explained by an illustration of flame evolution in a Borghi diagram.

Prechamber ignition↗
DOE OSTI2018

Mineralogical Controls on Frictional Strength, Stability, and Shear Permeability Evolution of Fractures

Massive fluid injection into the subsurface can induce microearthquakes by reactivating preexisting faults or fractures as seismic or aseismic slip. Such seismic or aseismic shear deformationsmay result in different modes of permeability evolution. Previous experimental studies have explored frictional stability-permeability relationships of carbonate-rich and phyllosilicate-rich samples under shear, suggesting that friction-permeability relationship may be primarily controlled by fracture minerals. We examine this relationship and identify the role of mineralogy (i.e., tectosilicate, carbonate, and phyllosilicate content) using direct-shear experiments on smooth saw-cut fractures of natural rocks and sintered fractures with distinct mineralogical compositions. These results indicate that the friction-permeability relationship is controlled by mineralogy. Frictional strength and permeability change upon reactivation decrease with phyllosilicate content but increase with tectosilicate content. In contrast, the reverse trend is observed for frictional stability (a-b). However, the permeability change decreases with carbonate content while both frictional strength and stability increase. The permeability change always decreases with an increase in frictional stability. This relationship implies a new mechanical-hydrochemical coupling loop via a linkage of frictional properties, mineralogy, and permeability.

58 GEOSCIENCES↗
DOE OSTI2020

Synthetic hybrids of six yeast species

Abstract Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Potentiating antibiotic efficacy via perturbation of non-essential gene expression

Proliferation of multidrug-resistant (MDR) bacteria poses a threat to human health, requiring new strategies. Here we propose using fitness neutral gene expression perturbations to potentiate antibiotics. We systematically explored 270 gene knockout-antibiotic combinations in Escherichia coli, identifying 90 synergistic interactions. Identified gene targets were subsequently tested for antibiotic synergy on the transcriptomic level via multiplexed CRISPR-dCas9 and showed successful sensitization of E. coli without a separate fitness cost. These fitness neutral gene perturbations worked as co-therapies in reducing a Salmonella enterica intracellular infection in HeLa. Finally, these results informed the design of four antisense peptide nucleic acid (PNA) co-therapies, csgD, fnr, recA and acrA, against four MDR, clinically isolated bacteria. PNA combined with sub-minimal inhibitory concentrations of trimethoprim against two isolates of Klebsiella pneumoniae and E. coli showed three cases of re-sensitization with minimal fitness impacts. Our results highlight a promising approach for extending the utility of current antibiotics.

60 APPLIED LIFE SCIENCES↗