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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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337 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

Abstract Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗
DOE OSTI2024

Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States

ABSTRACT Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified ( ƒ nitrified ), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta‐glucosidase (BG) and N ‐acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver of ƒ nitrified across regions, whereby increasing soil C resulted in a decline in net nitrification and ƒ nitrified . The ƒ nitrified value increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increased ƒ nitrified , including for high soil C sites predicted to have low ƒ nitrified , which decreased the role of soil C as a predictor of ƒ nitrified . Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID‐19 pandemic did not weaken the effect of N deposition on relationships between soil C and ƒ nitrified . Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems.

Nieland, Matthew A. [Stockbridge School of Agricul↗
DOE OSTI2026

Data for The Value of Reversible Carbon Storage in a Zero-Emissions World

Atmospheric carbon dioxide removal (CDR) is required to stabilize global temperature. CDR can be achieved via ecosystem-based approaches that are cost-effective but reversible (e.g., soil and forest management) or by more durable but expensive approaches (e.g., direct air capture coupled with geologic storage). Here, we examine trade-offs between these approaches, focusing on timing, climate impacts, and cost. We simulated reversible carbon accrual for a range of CDR contract structures using a general minimalist model of ecosystem carbon cycling, and parameterized it to simulate US agricultural soil management─specifically cover cropping─as a case study. We then quantified the resulting impact on atmospheric carbon and global temperature using a climate model emulator. We find that maintaining a patchwork of reversible CDR projects by replacing lapsed projects with new projects can reduce warming by 22–195 μ°C in 2100 and that the magnitude of this cooling effect depends on how effectively the patchwork is maintained. Long-term maintenance of reversible CDR projects requires institutional stability that cannot be guaranteed over multiple decades. Consequently, effective CDR ultimately requires replacing reversible projects with durable projects. To address this problem, we modeled the cost of replacing reversible agricultural soil CDR with geologic CDR. We found that using reversible CDR as a bridge to durable CDR is potentially more cost-effective as a global cooling strategy (0.20–0.81 billion USD per μ°C avoided) than perpetual maintenance of reversible CDR (0.32–1.31 billion USD per μ°C avoided) or an immediate transition to durable CDR (1.37–2.19 billion USD per μ°C avoided). However, we emphasize that institutional commitments to maintain reversible CDR projects cannot be guaranteed. Reliance on reversible CDR as a bridge to durable CDR therefore carries an unknown amount of risk and will only function if efforts to maintain reversible CDR are robust.

Carbon↗
DOE OSTI2025

Code associated with "Assessing the Effect of a Deep-Rooted Grass on Belowground Carbon Storage in Cultivated Land: Insights from a Multi-Site US Study"

R code associated with "Assessing the Effect of a Deep-Rooted Grass on Belowground Carbon Storage in Cultivated Land: Insights from a Multi-Site US Study" These scripts can be used to analyze the accompanying dataset: https://doi.org/10.5281/zenodo.16620529. (1) resampling_functions.R : Creates functions for resampling data for nonparametric bootstrapping (2) bootstrap_depth_profiles.R : Applies resampling functions to the dataset (3) gapfill_masscalcs.R : Prepares data for equivalent mass calculations (4) get_14C_EM.R : Applies soilR to obtain the 14C end member for mixing model calculations (5) mass_aggregate.R : Performs equivalent mass and mass weighted averaging calculations.

Carbon↗
DOE OSTI2025

YeastWGD2025

Supplementary data for Discovery of additional ancient genome duplications in yeasts wgd_syn / - directory containing wgd syn output for all contiguous genomes [dataset] Tree - phylogeny [dataset]Duplications - duplication table from OrthoFinder output KOannotations - KEGG annotations used for enrichment analysis IPRannotations - InterPro annotations used for enrichment analysis DipodascalesOrthogroups - formatted orthogroup assignments for Dipodascales genes.fa and .gff3 files for each new genome assembly are also provided, those these are not required to replicate the analysis

Genomics↗
DOE OSTI2025

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population

Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.

Evolutionary Biology↗
DOE OSTI2024

Y1000 gene family

All relative analysis data and codes used in this study are available on the Figshare data repository. You can also find the codes on the Github repository at https://github.com/vnuii/Y1000_gene_family.

budding yeast↗
DOE OSTI2025

Bulk segregant and QTL analysis of maltose metabolism in Saccharomyces eubayanus

This study investigates natural variation in maltose utilization among Saccharomyces eubayanus strains isolated from different tree hosts. An F2 population was generated from a cross between strain QC18 (Quercus-associated) and strain CL467.1 (Nothofagus-associated). Bulk segregant analysis (BSA) was performed on the F2 offspring, and QTL mapping was conducted by whole-genome sequencing of two pools of 30 segregants each, representing the lowest and highest growth in high maltose concentrations. For QTL analysis, the parental strains QC18 and CL467.1 were also sequenced.

evolutionary plasticity↗