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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales

Abstract There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evolutionary consequences of nascent multicellular life cycles

A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, although this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally reproducing ‘snowflake’ yeast (Δace2/∆ace2) and aggregative ‘floc’ yeast (GAL1p::FLO1 /GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of Darwinian individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift—a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2021

The effects of allelochemical transfer on the dynamics of hosts, parasitoids, and competing hyperparasitoids

Allelochemicals produced by plants may be ingested by herbivorous insects and transferred to higher trophic levels with potentially deleterious effects. We develop a system of differential equations to investigate the effect of the transfer of allelochemicals, such as nicotine, on the population dynamics of a system of hosts, parasitoids, and two competing hyperparasitoids that attack different life stages of the parasitoids. We find both somewhat deleterious effects of nicotine on the larvae-attacking hyperparasitoids and increased attack rates for the pupae-attacking hyperparasitoids can promote coexistence. We also use an evolutionary game-theoretic approach to determine the optimal distribution of hyperparasitoid attacks among nicotine-producing and nicotine-free plants. With strong deleterious effects of nicotine and increased attack rates for the pupae-attacking hyperparasitoid, we find both species attack parasitoids on the nicotine-free plant but only pupae-attacking hyperparasitoids attack parasitoids on the nicotine-producing plant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Computational Modeling and Evolutionary Implications of Biochemical Reactions in Bacterial Microcompartments

Bacterial microcompartments (BMCs) are protein-encapsulated compartments found across at least 23 bacterial phyla. BMCs contain a variety of metabolic processes that share the commonality of toxic or volatile intermediates, oxygen-sensitive enzymes and cofactors, or increased substrate concentration for magnified reaction rates. These compartmentalized reactions have been computationally modeled to explore the encapsulated dynamics, ask evolutionary-based questions, and develop a more systematic understanding required for the engineering of novel BMCs. Many crucial aspects of these systems remain unknown or unmeasured, such as substrate permeabilities across the protein shell, feasibility of pH gradients, and transport rates of associated substrates into the cell. This review explores existing BMC models, dominated in the literature by cyanobacterial carboxysomes, and highlights potentially important areas for exploration.

bacterial microcompartments↗
DOE OSTI2021

Mutations in artificial self-replicating tiles: A step toward Darwinian evolution

Significance In nature, mutation is the first step of evolution, where it provides the genetic variation for the natural selection to act. Here we take a system of artificial self-replicating tiles, DNA origami, that exhibit templated reproduction. We can generate a small fraction of mutations by introducing a mismatch in hybridization between parent and daughter. We can modify the origami functionality to affect the growth rate of the mutated species, giving it less or more evolutionary advantage, and to become dominant in several generations. The introduction of mutations into an artificial self-replicating system provides new directions for research into self-assembly processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

A trait syndrome ties cell morphology to glycolysis across the yeast subphylum

Co-variation of traits provides fundamental insights into constraints governing their evolution. An inverse correlation between glucose uptake rates (GURs) and cell surface area-to-volume (SA:V) ratios across 11 yeast species was recently reported. Here, we expand the analysis to 282 species to assess the generalizability of this correlation across Saccharomycotina yeasts and the contribution of shared evolutionary history to the co-variation of these traits. Using phylogenetic regression models, we found extracellular acidification rates (ECARs, used as a proxy for GURs) were weakly, but significantly, correlated with SA:V across Saccharomycotina. ECARs were also correlated with genome sizes and growth rates. Our findings support the reported correlation between GURs and SA:V ratios, but suggest other associated traits, including genome sizes. Specifically, yeasts that consume glucose faster tend to have lower SA:V, faster growth rates, and larger genomes, suggesting a trait syndrome governing several metabolic, genomic, and morphological traits across the yeast subphylum.

biological sciences↗
DOE OSTI2021

2M17091769+3127589: A Mass-transfer Binary with an Extreme Mass Ratio

We present the orbital solution of a peculiar double-lined spectroscopic and eclipsing binary system, 2M17091769+3127589. This solution was obtained by a simultaneous fit of both APOGEE radial velocities and TESS and ASAS-SN light curves to determine masses and radii. This system consists of an M=0.256{sub -0.006}{sup +0.010} M {sub ⊙}, R=3.961{sub -0.032}{sup +0.049} R {sub ⊙} red giant and a hotter M=1.518{sub -0.031}{sup +0.057} M {sub ⊙}, R=2.608{sub -0.321}{sup +0.034} R {sub ⊙} subgiant. Modeling with the MESA evolutionary codes indicates that the system likely formed 5.26 Gyrs ago, with a M = 1.2 M {sub ⊙} primary that is now the system’s red giant and a M = 1.11 M {sub ⊙} secondary that is now a more massive subgiant. Due to Roche-lobe overflow as the primary ascends the red giant branch, the more evolved “primary” (i.e., originally the more massive star of the pair) is now only one sixth as massive as the “secondary.” Such a difference between the initial and the current mass ratio is one of the most extreme detected so far. Evolutionary modeling suggests the system is still engaged in mass transfer, at a rate of M-dot ~10{sup -9} M {sub ⊙}/yr, and it provides an example of a less evolved precursor to some of the systems that consist of white dwarfs and blue stragglers.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Aggressively Dissipative Dark Dwarfs: The Effects of Atomic Dark Matter on the Inner Densities of Isolated Dwarf Galaxies

We present the first suite of cosmological hydrodynamical zoom-in simulations of isolated dwarf galaxies for a dark sector that consists of cold dark matter and a strongly dissipative subcomponent. The simulations are implemented in GIZMO and include standard baryons following the FIRE-2 galaxy formation physics model. The dissipative dark matter is modeled as atomic dark matter (aDM), which forms a dark hydrogen gas that cools in direct analogy to the Standard Model. Our suite includes seven different simulations of ∼10 10 M ⊙ systems that vary over the aDM microphysics and the dwarf’s evolutionary history. We identify a region of aDM parameter space where the cooling rate is aggressive and the resulting halo density profile is universal. In this regime, the aDM gas cools rapidly at high redshifts, and only a small fraction survives in the form of a central dark gas disk; the majority collapses centrally into collisionless dark “clumps,” which are clusters of subresolution dark compact objects. These dark clumps rapidly equilibrate in the inner galaxy, resulting in an approximately isothermal distribution that can be modeled with a simple fitting function. Even when only a small fraction (∼5%) of the total dark matter is strongly dissipative, the central densities of classical dwarf galaxies can be enhanced by over an order of magnitude, providing a sharp prediction for observations.

cold dark matter↗
DOE OSTI2022

Relation of Observable Stellar Parameters to Mass-loss Rate of AGB Stars in the LMC

Using the data set of Riebel et al. for 6889 pulsating AGB stars in the LMC, we have derived formulae for mass-loss rate as a function of luminosity and pulsation period, or luminosity and mass, in three ways, for each of five subsets of data: fundamental-mode oxygen-rich stars, first-overtone-mode oxygen-rich stars, fundamental-mode carbon stars, first-overtone-mode carbon stars, and extreme carbon stars. Using the distribution of the stars in period versus luminosity and mass versus luminosity, we are able to derive a power-law fit to the dependence of mass-loss rate on those quantities. This results in formulae that reproduce observed mass-loss rates and are in general agreement with the expectation from mass-loss models that the mass-loss rate is highly sensitive to luminosity, mass, and pulsation period. In the process of carrying out this analysis we have found radius–mass–luminosity relations and examined pulsation–mass–radius relations using published evolutionary and pulsation models. These allow us to derive mass and radius from the observed quantities luminosity and pulsation period. We also derived new mass-loss rate versus color relations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Microbial Evolution Drives Adaptation of Substrate Degradation on Decadal to Centennial Time Scales Relevant to Global Change

ABSTRACT Understanding microbial adaptation is crucial for predicting how soil carbon dynamics and global biogeochemical cycles will respond to climate change. This study employs the DEMENT model of microbial decomposition, along with empirical mutation and dispersal rates, to explore the roles of mutation and dispersal in the adaptation of soil microbial populations to shifts in litter chemistry, changes that are anticipated with climate‐driven vegetation dynamics. Following a change in litter chemistry, mutation generally allows for a higher rate of litter decomposition than dispersal, especially when dispersal predominantly introduces genotypes already present in the population. These findings challenge the common idea that mutation rates are too low to affect ecosystem processes on ecological timescales. These results demonstrate that evolutionary processes, such as mutation, can help maintain ecosystem functioning as the climate changes.

Abs, Elsa↗
DOE OSTI2024

Emergence of catalytic function in prebiotic information-coding polymers

Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Emergence of catalytic function in prebiotic information-coding polymers

Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.

Tkachenko, Alexei V. (ORCID:000000031291243X)↗
DOE OSTI2022

Dynamical Unification of Tidal Disruption Events

The ~100 tidal disruption events (TDEs) observed so far exhibit a wide range of emission properties both at peak and over their lifetimes. Some TDEs radiate predominantly at X-ray energies, while others radiate chiefly at UV and optical wavelengths. While the peak luminosities across TDEs show distinct properties, the evolutionary behavior can also vary between TDEs with similar peak emission properties. In particular, for optical TDEs, while their UV and optical emissions decline somewhat following the fallback pattern, some events can greatly rebrighten in X-rays at late time. In this Letter, we conduct three-dimensional general relativistic radiation magnetohydrodynamics simulations of TDE accretion disks at varying accretion rates in the regime of super-Eddington accretion. We make use of Monte Carlo radiative transfer simulations to calculate the reprocessed spectra at various inclinations and at different evolutionary stages. We confirm the unified model proposed by Dai et al., which predicts that the observed emission largely depends on the viewing angle of the observer with respect to the disk orientation. Furthermore, we find that disks with higher accretion rates have elevated wind and disk densities, which increases the reprocessing of the high-energy radiation and thus generally augments the optical-to-X-ray flux ratio along a particular viewing angle. This implies that at later times, as the accretion level declines, we expect that more X-rays will leak out along intermediate viewing angles. Such dynamical model for TDEs can provide a natural explanation for the diversity in the emission properties observed in TDEs at peak and along their temporal evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Evolutionary History of Plant Metabolism

Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO 2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.

Plant Sciences↗
DOE OSTI2026

Convergent evolution of aerobic fermentation through divergent mechanisms acting on key shared glycolytic genes

As the tree of life becomes increasingly accessible to molecular investigations, describing mechanisms underlying evolutionary convergence and constraint will be crucial to understanding diversification. The lineage including the model yeast Saccharomyces cerevisiae evolved aerobic fermentation in part through an ancient whole genome duplication and retention of glycolytic genes. To evaluate glycolytic rates across diverse yeasts, we developed and deployed an extracellular acidification rates (ECAR) assay on 299 species that span more than 400 million years of evolution and identified a clade in the genus Saturnispora that convergently evolved aerobic fermentation. Through comparative genomics and transcriptomics, we found that several glycolytic genes had higher expression and novel cis-regulatory elements in aerobically fermenting Saturnispora species. When the transcription factor required for their activation was deleted in Saturnispora dispora, the mutants had reduced glycolytic rates and increased respiration. Intriguingly, many of the upregulated genes are orthologous to duplicated glycolytic genes in S. cerevisiae. These divergent genetic mechanisms affecting the same set of genes suggest that there are strong evolutionary constraints on how aerobic fermentation can arise.

Horianopoulos, Linda C. [Great Lakes Bioenergy Res↗
DOE OSTI2021

The growth of intracluster light in XCS-HSC galaxy clusters from 0.1 < z < 0.5

ABSTRACT We estimate the intracluster light (ICL) component within a sample of 18 clusters detected in the XMM Cluster Survey (XCS) data using the deep (∼26.8 mag) Hyper Suprime-Cam Subaru Strategic Programme data release 1 i-band data. We apply a rest-frame μB = 25 mag arcsec−2 isophotal threshold to our clusters, below which we define light as the ICL within an aperture of RX,500 (X-ray estimate of R500) centred on the brightest cluster galaxy (BCG). After applying careful masking and corrections for flux losses from background subtraction, we recover ∼20 per cent of the ICL flux, approximately four times our estimate of the typical background at the same isophotal level (${\sim}5{{\ \rm per\ cent}}$). We find that the ICL makes up about ${\sim}24{{\ \rm per\ cent}}$ of the total cluster stellar mass on average (∼41 per cent including the flux contained in the BCG within 50 kpc); this value is well matched with other observational studies and semi-analytic/numerical simulations, but is significantly smaller than results from recent hydrodynamical simulations (even when measured in an observationally consistent way). We find no evidence for any links between the amount of ICL flux with cluster mass, but find a growth rate of 2–4 for the ICL between 0.1 < z < 0.5. We conclude that the ICL is the dominant evolutionary component of stellar mass in clusters from z ∼ 1. Our work highlights the need for a consistent approach when measuring ICL alongside the need for deeper imaging, in order to unambiguously measure the ICL across as broad a redshift range as possible (e.g. 10-yr stacked imaging from the Vera C. Rubin Observatory).

Furnell, Kate E.↗
DOE OSTI2024

Homologous recombination shapes the architecture and evolution of bacterial genomes

Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotspots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.

Torrance, Ellis L [University of North Carolina, G↗
DOE OSTI2021

Price equation captures the role of drug interactions and collateral effects in the evolution of multidrug resistance

Bacterial adaptation to antibiotic combinations depends on the joint inhibitory effects of the two drugs (drug interaction [DI]) and how resistance to one drug impacts resistance to the other (collateral effects [CE]). Here we model these evolutionary dynamics on two-dimensional phenotype spaces that leverage scaling relations between the drug-response surfaces of drug-sensitive (ancestral) and drug-resistant (mutant) populations. We show that evolved resistance to the component drugs – and in turn, the adaptation of growth rate – is governed by a Price equation whose covariance terms encode geometric features of both the two-drug-response surface (DI) in ancestral cells and the correlations between resistance levels to those drugs (CE). Within this framework, mean evolutionary trajectories reduce to a type of weighted gradient dynamics, with the drug interaction dictating the shape of the underlying landscape and the collateral effects constraining the motion on those landscapes. We also demonstrate how constraints on available mutational pathways can be incorporated into the framework, adding a third key driver of evolution. Our results clarify the complex relationship between drug interactions and collateral effects in multidrug environments and illustrate how specific dosage combinations can shift the weighting of these two effects, leading to different and temporally explicit selective outcomes.

Gjini, Erida↗