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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

Cacao pod transcriptome profiling of seven genotypes identifies features associated with post-penetration resistance to Phytophthora palmivora

Abstract The oomycete Phytophthora palmivora infects the fruit of cacao trees ( Theobroma cacao ) causing black pod rot and reducing yields. Cacao genotypes vary in their resistance levels to P. palmivora , yet our understanding of how cacao fruit respond to the pathogen at the molecular level during disease establishment is limited. To address this issue, disease development and RNA-Seq studies were conducted on pods of seven cacao genotypes (ICS1, WFT, Gu133, Spa9, CCN51, Sca6 and Pound7) to better understand their reactions to the post-penetration stage of P. palmivora infection. The pod tissue- P. palmivora pathogen assay resulted in the genotypes being classified as susceptible (ICS1, WFT, Gu133 and Spa9) or resistant (CCN51, Sca6 and Pound7). The number of differentially expressed genes (DEGs) ranged from 1625 to 6957 depending on genotype. A custom gene correlation approach identified 34 correlation groups. De novo motif analysis was conducted on upstream promoter sequences of differentially expressed genes, identifying 76 novel motifs, 31 of which were over-represented in the upstream sequences of correlation groups and associated with gene ontology terms related to oxidative stress response, defense against fungal pathogens, general metabolism and cell function. Genes in one correlation group (Group 6) were strongly induced in all genotypes and enriched in genes annotated with defense-responsive terms. Expression pattern profiling revealed that genes in Group 6 were induced to higher levels in the resistant genotypes. An additional analysis allowed the identification of 17 candidate cis -regulatory modules likely to be involved in cacao defense against P. palmivora . This study is a comprehensive exploration of the cacao pod transcriptional response to P. palmivora spread after infection. We identified cacao genes, promoter motifs, and promoter motif combinations associated with post-penetration resistance to P. palmivora in cacao pods and provide this information as a resource to support future and ongoing efforts to breed P. palmivora -resistant cacao.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Activated penetrant dynamics in glass forming liquids: size effects, decoupling, slaving, collective elasticity and correlation with matrix compressibility

In this work, we employ the microscopic self-consistent cooperative hopping theory of penetrant activated dynamics in glass forming viscous liquids and colloidal suspensions to address new questions over a wide range of high matrix packing fractions and penetrant-to-matrix particle size ratios. The focus is on the mean activated relaxation time of smaller tracers in a hard sphere fluid of larger particle matrices. This quantity also determines the penetrant diffusion constant and connects directly with the structural relaxation time probed in an incoherent dynamic structure factor measurement. The timescale of the non-activated fast dissipative process is also studied and is predicted to follow power laws with the contact value of the penetrant–matrix pair correlation function and the penetrant–matrix size ratio. For long time penetrant relaxation, in the relatively lower packing fraction metastable regime the local cage barriers are dominant and matrix collective elasticity effects unimportant. As packing fraction and/or penetrant size grows, much higher barriers emerge and the collective elasticity associated with the correlated matrix dynamic displacement that facilitates penetrant hopping becomes important. This results in a non-monotonic variation with packing fraction of the degree of decoupling between the matrix and penetrant alpha relaxation times. The conditions required for penetrant hopping to become slaved to the matrix alpha process are determined, which depend mainly on the penetrant to matrix particle size ratio. By analyzing the absolute and relative importance of the cage and elastic barriers we establish a mechanistic understanding of the origin of the predicted exponential growth of the penetrant hopping time with size ratio predicted at very high packing fractions. A dynamics-thermodynamics power law connection between the penetrant activation barrier and the matrix dimensionless compressibility is established as a prediction of theory, with different scaling exponents depending on whether matrix collective elasticity effects are important. Quantitative comparisons with simulations of the penetrant relaxation time, diffusion constant, and transient localization length of tracers in dense colloidal suspensions and cold viscous liquids reveal good agreements. Multiple new predictions are made that are testable via future experiments and simulations. Extension of the theoretical approach to more complex systems of high experimental interest (nonspherical molecules, semiflexible polymers, crosslinked networks) interacting via variable hard or soft repulsions and/or short range attractions is possible, including under external deformation.

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

Exploring Hydrologic Model Process Connectivity at the Continental Scale Through an Information Theory Approach

Exploring water fluxes between hydrological model (HM) components is essential to assess and improve model realism. Many classical metrics for HM diagnosis rely solely on streamflow and hence provide limited insights into model performance across processes. This study applies an information theory measure known as “transfer entropy” (TE) to systematically quantify the transfer of information among major HM components. To test and demonstrate the benefits of TE, we use the Framework for Understanding Structural Errors (FUSE) model to mimic and compare four commonly used HM structures, VIC, PRMS, SACRAMENTO, and TOPMODEL, across 671 catchments spanning a variety of hydrologic regimes in the conterminous United States. We explore connections between HM components and catchment landscape characteristics (e.g., climate, topography, soil, and vegetation) and characterize their nonlinear associations using distance correlation and Spearman correlation coefficients. Our results indicate that while the information transferred from precipitation to runoff is similar across model structures (likely as a result of calibration), the information transferred among other components can vary significantly from a FUSE structure to another. We find that aridity, precipitation duration and frequency, snow fraction, mean elevation, forest area, and leaf area index are often significantly associated with TE between the main HM components. Here, we propose that the presence of meaningful nonlinear associations can be used to diagnose process representation in HMs. Our results highlight the necessity to enhance the conventional streamflow-only calibration approach for a more realistic representation of water dynamics in the models.

large-sample hydrology↗
DOE OSTI2022

Assessing the large-scale drivers of precipitation in the northeastern United States via linear orthogonal decomposition

This study examines the linear orthogonal modes associated with monthly precipitation in the northeastern United States, from CESM1 LENS (35 ensemble members, 1979–2005) and two reanalysis datasets (ERA5, 1950–2018 and NOAA-CIRES-DOE 20CRv3, 1950–2015). Calendar months are aggregated together, and any linear trends in data are removed. Using region-averaged precipitation anomaly time series and monthly anomalies for several global 2D atmospheric fields, a linear orthogonal decomposition method is implemented to iteratively extract time series (based on field and geographic location) of absolute maximum correlation. Linear modes associated with this method are then projected onto the full set of 2D fields to provide physical insight into the mechanisms involved in generating precipitation. In this region, the first mode is associated with vapor transport from the Atlantic seaboard, the second mode is characterized by westward vapor transport associated with extratropical cyclones, and the third mode captures vapor transport from the Gulf of Mexico during the fall and winter. However, the third mode is less robust in the spring and summer. Results are generally consistent across the datasets, and applying multiple linear regression with the linear modes to predict the precipitation anomalies produces R-squared values of around 0.54–0.65 for CESM1 LENS, and around 0.58–0.88 for reanalysis, with the lowest values generally in the spring and late summer. The influence of low-frequency climate variability on the modes is considered for CESM1 LENS, and the modes in late winter can be predicted with some success via a combination of several, prominent large-scale teleconnection patterns.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Measurement of D 0 -meson + hadron two-dimensional angular correlations in Au + Au collisions at s N N = 200 GeV

Open heavy flavor hadrons provide unique probes of the medium produced in ultra-relativistic heavy-ion collisions. Due to their increased mass relative to light-flavor hadrons, long lifetime, and early production in hard-scattering interactions, they provide access to the full evolution of the partonic medium formed in heavy-ion collisions. This paper reports two-dimensional (2D) angular correlations between neutral D-mesons and unidentified charged particles produced in minimum-bias Au+Au collisions at s N N = 200 GeV. D 0 and D 0 ¯ mesons are reconstructed via their weak decay to K ∓ π ± using the Heavy Flavor Tracker (HFT) in the Solenoidal Tracker at RHIC (STAR) experiment. Correlations on relative pseudorapidity and azimuth (Δη,ΔΦ) are presented for peripheral, mid-central and central collisions with D 0 transverse momentum from 2 to 10 GeV/c. Attention is focused on the 2D peaked correlation structure near the triggered D 0 -meson, the {\em near-side} (NS) peak, which serves as a proxy for a charm-quark containing jet. The correlated NS yield of charged particles per D 0 -meson and the 2D widths of the NS peak increase significantly from peripheral to central collisions. These results are compared with similar correlations using unidentified charged particles, consisting primarily of light-flavor hadrons, at similar trigger particle momenta. Similar per-trigger yields and widths of the NS correlation peak are observed. Here, the present results provide additional evidence that D 0 -mesons undergo significant interactions with the medium formed in heavy-ion collision and show, for the first time, significant centrality evolution of the NS 2D peak in the correlations of particles associated with a heavy-flavor hadron produced in these collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Transcriptional networks underlying a primary ovarian insufficiency disorder in alligators naturally exposed to EDCs

Interactions between the endocrine system and environmental contaminants are responsible for impairing reproductive development and function. Despite the taxonomic diversity of affected species and attendant complexity inherent to natural systems, the underlying signaling pathways and cellular consequences are mostly studied in lab models. To resolve the genetic and endocrine pathways that mediate affected ovarian function in organisms exposed to endocrine disrupting contaminants in their natural environments, we assessed broad-scale transcriptional and steroidogenic responses to exogenous gonadotropin stimulation in juvenile alligators (Alligator missippiensis) originating from a lake with well-documented pollution (Lake Apopka, FL) and a nearby reference site (Lake Woodruff, FL). Here, we found that individuals from Lake Apopka are characterized by hyperandrogenism and display hyper-sensitive transcriptional responses to gonadotropin stimulation when compared to individuals from Lake Woodruff. Site-specific transcriptomic divergence appears to be driven by wholly distinct subsets of transcriptional regulators, indicating alterations to fundamental genetic pathways governing ovarian function. Consistent with broad-scale transcriptional differences, ovaries of Lake Apopka alligators displayed impediments to folliculogenesis, with larger germinal beds and decreased numbers of late-stage follicles. After resolving the ovarian transcriptome into clusters of co-expressed genes, most site-associated modules were correlated to ovarian follicule phenotypes across individuals. However, expression of two site-specific clusters were independent of ovarian cellular architecture and are hypothesized to represent alterations to cell-autonomous transcriptional programs. Collectively, our findings provide high resolution mapping of transcriptional patterns to specific reproductive function and advance our mechanistic understanding regarding impaired reproductive health in an established model of environmental endocrine disruption.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Interpolating individual line-of-sight neutron spectrometer measurements onto the “sky” at the National Ignition Facility (NIF)

Nuclear diagnostics provide measurements of inertial confinement fusion implosions used as metrics of performance for the shot. The interpretation of these measurements for shots with low mode asymmetries requires a way of combining the data to produce a “sky map” where the individual line-of-sight values are used to interpolate to other positions in the sky. These interpolations can provide information regarding the orientation of the low mode asymmetries. We describe the interpolation method, associated uncertainties, and correlations between different metrics, e.g., Tion, down scatter ratio, and hot-spot velocity direction. This work is also related to recently reported studies [H. G. Rinderknecht et al., Phys. Rev. Lett. 124, 145002 (2020) and K. M. Woo et al., Phys. Plasmas 27, 062702 (2020)] of low mode asymmetries. We report an analysis that makes use of a newly commissioned line of sight, a scheme for incorporating multiple neutron spectrum measurement types, and recent work on the sources of implosion asymmetry to provide a more complete picture of implosion performance.

Hartouni, E. P. (ORCID:0000000198694351)↗
DOE OSTI2023

X-ray induced electron and ion fragmentation dynamics in IBr

Characterization of the inner-shell decay processes in molecules containing heavy elements is key to understanding x-ray damage of molecules and materials and for medical applications with Auger-electron-emitting radionuclides. The 1s hole states of heavy atoms can be produced by absorption of tunable x rays and the resulting vacancy decays characterized by recording emitted photons, electrons, and ions. The 1s hole states in heavy elements have large x-ray fluorescence yields that transfer the hole to intermediate electron shells that then decay by sequential Auger-electron transitions that increase the ion’s charge state until the final state is reached. In molecules, the charge is spread across the atomic sites, resulting in dissociation to energetic atomic ions. We have used x-ray/ion coincidence spectroscopy to measure charge states and energies of Iq+ and Brq′+ atomic ions following 1s ionization at the I and Br K-edges of IBr. We present the charge states and kinetic energies of the two correlated fragment ions associated with core-excited states produced during the various steps of the cascades. Here, to understand the dynamics leading to the ion data, we develop a computational model that combines Monte-Carlo/Molecular-Dynamics (MC/MD) simulations with a classical over-the-barrier model to track inner-shell cascades and redistribution of electrons in valence orbitals and nuclear motion of fragments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Complex structure due to As bonding and interplay with electronic structure in superconducting BaNi 2 As 2

BaNi 2 As 2 is a superconductor chemically related to the Fe-based superconductors, with a complex and poorly understood structural phase transition. We show, based on first-principles calculations, that, in fact, there are two distinct competing structures. These structures are different from the electronic, transport, and bonding points of view but are close in energy. These arise due to complex As bonding patterns and drive distortions of the Ni layers. This is supported by photoemission experiments. This is very distinct from views of the distortion as being primarily driven by electrons at the Fermi surface as in a classical charge density wave, or by correlated electron physics associated with the Ni d electrons and the Ni d orbitals. The structural distortion, although connected with As does lead to an interplay of electronic and structural behavior including induced anisotropic electronic transport. Here, the local bonding nature of the instabilities and the competition between distortions is discussed in the context of the complex behavior observed in BaNi 2 As 2 samples.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Calculating n-point charge correlations in evolving systems

Background: In dynamic systems such as heavy-ion collisions, charge susceptibilities and local charge correlations change with time. These changes are accompanied by nonlocal correlations, which spread diffusively with time and are constrained by local charge conservation. Such correlations have been measured at the Relativistic Heavy-Ion Collider (RHIC) and have been linked to the chemical evolution of the matter and possible phase separation or critical phenomena. The evolution of such correlations has been modeled for two-point correlators superimposed onto hydrodynamics, but not for three- or four-point correlators. These higher-order correlators represent an essential basis for calculating the kurtosis and skewness of charge distributions measured at RHIC. For short-range correlations, such as those between charges on the same particle, and the associated charge-balance correlations a theoretical formalism was lacking for handling higher-order correlations. In particular, one needed to understand how higher-order charge fluctuations was split onto lower numbers of particles. For example, correlations of order three have contributions with charge all on one particle, split onto two particle, or split onto three. By assuming local chemical equilibrium of short-range correlations, the sources of the various correlators were found to be uniquely determined. The relevant theoretical foundation is presented here, including a diagrammatic technique to correctly account for all the possible terms to higher-order correlations. Here, we found a consistent theoretical treatment and its applicability, viability, and tractability are discussed. The formalism derived here enables realistic and quantitative modeling of the three- and four-point charge correlations necessary for understanding measurements of the kurtosis and skewness of charge distributions at RHIC. These observables have been promoted as signals of phase transitions or measures of chemical evolution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

High-Power Polyphase PCB-Type Inductive Coupler for Wireless Electric Vehicle Charging

The cost and manufacturing difficulty of traditionally wound coils for wireless charging of electric vehicles has led to the exploration of alternative manufacturing for scalable deployment at a range of rated powers. A rotating-field polyphase wireless coupler is developed with balanced fully pitched coils which are not possible with conventional Litz wire. The usage of printed circuit board (PCB) technology is proposed for the innovative construction at large dimensions due to reduced cost, increased ease of manufacturability, and potential geometric customization compared to would coils. Design considerations specific to PCBs are detailed for wireless power transfer coils including advantages such as the potential for many turns and transposition with planar interconnections. A design procedure is developed which may be used to investigate the frequency to power to dimension correlation and limits associated with PCB coils. Designs are simulated in 3D electromagnetic finite element analysis (FEA) for the polyphase coil to evaluate the coupling between coils with varying geometric parameters at 100mm and 500mm outer diameters. A discussion is included on methods to increase PCB power ratings through a mixture of layer stacking, connections, and material selection.

Lewis, Donovin D.↗
DOE OSTI2021

Distinct Clinical Impact and Biological Function of Angiopoietin and Angiopoietin-like Proteins in Human Breast Cancer

Secreted angiopoietin/angiopoietin-like (ANGPT/ANGPTL) proteins are involved in many biological processes. However, the role of these proteins in human breast cancers (BCs) remains largely unclear. Here, we conducted integrated omics analyses to evaluate the clinical impact of ANGPT/ANGPTL proteins and to elucidate their biological functions. In BCs, we identified rare mutations in ANGPT/ANGPTL genes, frequent gains of ANGPT1, ANGPT4, and ANGPTL1, and frequent losses of ANGPT2, ANGPTL5, and ANGPTL7, but observed that ANGPTL1, 2, and 4 were robustly downregulated in multiple datasets. The expression levels of ANGPTL1, 5, and 8 were positively correlated with overall survival (OS), while the expression levels of ANGPTL4 were negatively correlated with OS. Additionally, the expression levels of ANGPTL1 and 7 were positively correlated with distant metastasis-free survival (DMFS), while the expression levels of ANGPT2 and ANGPTL4 were negatively correlated with DMFS. The prognostic impacts of ANGPT/ANGPTL genes depended on the molecular subtypes and on clinical factors. We discovered that various ANGPT/ANGPTL genes were co-expressed with various genes involved in different pathways. Finally, with the exception of ANGPTL3, the remaining genes showed significant correlations with cancer-associated fibroblasts, endothelial cells, and microenvironment score, whereas only ANGPTL6 was significantly correlated with immune score. Our findings provide strong evidence for the distinct clinical impact and biological function of ANGPT/ANGPTL proteins, but the question of whether some of them could be potential therapeutic targets still needs further investigation in BCs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Linking Hydrology and Dissolved Organic Matter Characteristics in a Subtropical Wetland: A Long-Term Study of the Florida Everglades

Dissolved organic matter (DOM) acts as an important biogeochemical component of aquatic ecosystems that controls nutrient cycling, influences water quality, and links terrestrial and oceanic carbon pools, yet long-term studies of how changing environmental drivers alter its abundance and composition are rare. Using a ten-year, spatially explicit dataset from Everglades National Park (ENP), a globally significant wetland, we investigated the relationships between DOM quality/quantity and hydrologic/climatic drivers along two contrasting marsh-estuarine transects based on generalized linear modeling and a cumulative sums analysis. Analyses revealed distinct spatial, seasonal, and interannual patterns in variability of DOC and optical properties. Landscape-scale seasonal patterns showed an enrichment in microbial-like and protein-like DOM during the dry season relative to the wet season. We found that, while some compositional constituents varied with the solar calendar, responsive to temperature and photoperiod, others varied with the hydrologic calendar. Independent water level and discharge effects indicated strong hydrologic control on DOM quality that differed between the two transects, evidencing differences in their connectivity to areas of high agricultural activity. Across all sites, a significant long-term increasing trend in the fluorescence index was observed, associated with a positive correlation with precipitation and also potential changes in agricultural inputs, with other features associated with drought and hurricanes. Lastly, the cumulative sums analysis revealed differences between the two transects in the sensitivity of DOM composition to decreased water levels associated with 30-year climate scenarios, with the less hydrologically dynamic transect exhibiting greater potential sensitivity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Characterizing initial- and final-state effects of relativistic nuclear collisions

Here, the multiphase transport model (AMPT) is used to study the final-state effects on the symmetric correlations (SC), asymmetric correlations (ASC), normalized symmetric correlations (NSC), and normalized asymmetric correlations (NASC) in Au+Au collisions at 200 GeV. The correlators' sensitivity to nonflow effects associated with long- and short-range nonflow correlations are also discussed using the HIJING model. The results indicate that SC, ASC, NSC, and NASC can give accompanying constraints for initial- and final-state effects. In addition, conducting further detailed experimental measurements spanning a broad range of collision systems and beam energies will serve as an additional constraint for the theoretical models' calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Field-Driven Simulations to Probe the Impact of Ionic Correlations on Solution Transport Coefficients in Binary, Ternary, and Reciprocal Quaternary Aqueous Electrolytes

Ionic correlations play a critical role in governing transport properties of mixed-salt aqueous electrolyte solutions, yet their quantitative characterization remains challenging, particularly for multicomponent aqueous systems. Here, we develop a general nonequilibrium molecular dynamics framework to efficiently compute Onsager transport coefficients and ionic correlations in mixed-salt aqueous solutions. Using field-driven simulations, we obtain accurate Onsager matrices for LiCl/ KCl, KCl/KBr, and LiBr/KCl electrolyte solutions with significantly reduced computational cost relative to equilibrium Green−Kubo methods. The framework enables direct assessment of how attractive cation−anion and repulsive like-ion interactions contribute to conductivity and salt diffusivity across compositions. While static ion pairing exhibits strong composition dependence, dynamic ion correlations remain nearly invariant, leading to constant deviations from Nernst−Einstein predictions. These results highlight the disconnect between static ion association and dynamic transport correlations, and they establish a transferable approach for analyzing ion transport in complex electrolyte environments relevant to separation processes and electrochemical systems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

On the quenching of star formation in observed and simulated central galaxies: evidence for the role of integrated AGN feedback

ABSTRACT In this paper, we investigate how massive central galaxies cease their star formation by comparing theoretical predictions from cosmological simulations: EAGLE, Illustris, and IllustrisTNG with observations of the local Universe from the Sloan Digital Sky Survey (SDSS). Our machine learning (ML) classification reveals supermassive black hole mass (MBH) as the most predictive parameter in determining whether a galaxy is star forming or quenched at redshift z = 0 in all three simulations. This predicted consequence of active galactic nucleus (AGN) quenching is reflected in the observations, where it is true for a range of indirect estimates of MBH via proxies as well as its dynamical measurements. Our partial correlation analysis shows that other galactic parameters lose their strong association with quiescence, once their correlations with MBH are accounted for. In simulations, we demonstrate that it is the integrated power output of the AGN, rather than its instantaneous activity, which causes galaxies to quench. Finally, we analyse the change in molecular gas content of galaxies from star-forming to passive populations. We find that both gas fractions (fgas) and star formation efficiencies (SFEs) decrease upon transition to quiescence in the observations but SFE is more predictive than fgas in the ML passive/star-forming classification. These trends in the SDSS are most closely recovered in IllustrisTNG and are in direct contrast with the predictions made by Illustris. We conclude that a viable AGN feedback prescription can be achieved by a combination of preventative feedback and turbulence injection which together quench star formation in central galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Long range energy-energy correlator at the LHC

We study the forward-backward azimuthal angular correlations of hadrons in association with multiparticle production in the central rapidity region in proton-proton collisions at the LHC. We apply the nucleon energy-energy correlator framework, where the spinning gluon distribution introduces a nontrivial cos⁡(2⁢𝜙) asymmetries. We will demonstrate that the fundamental helicity structure of quantym chromodynamics (QCD) amplitudes predicts a unique power counting rule: cos⁡(2⁢𝜙) asymmetry starts at 𝒪⁡(𝛼$^{2}_{s}$) order for dijet, 𝒪⁡(𝛼 𝑠 ) for three jet and 𝒪⁡(1) for four (and more) jet productions. Our results will help us to understand the longstanding puzzle of nearside ridge behavior observed in high multiplicity events of 𝑝⁢𝑝 collisions at the LHC.

Quantum chromodynamics↗
DOE OSTI2021

Signatures of optimal codon usage in metabolic genes inform budding yeast ecology

Reverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism ( GAL ) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in the GAL pathway is positively correlated with quantitative growth on galactose, suggesting that GAL codon optimization reflects increased capacity to grow on galactose. Optimal codon usage in the GAL pathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage of GAL genes is greater than 85% of all genes in the genome of the major human pathogen Candida albicans (CUG-Ser1 clade) and greater than 75% of genes in the genome of the dairy yeast Kluyveromyces lactis (family Saccharomycetaceae). We further find a correlation between optimization in the GAL actose pathway genes and several genes associated with nutrient sensing and metabolism. This work suggests that codon optimization harbors information about the metabolic ecology of microbial eukaryotes. This information may be particularly useful for studying fungal dark matter—species that have yet to be cultured in the lab or have only been identified by genomic material.

59 BASIC BIOLOGICAL SCIENCES↗