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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping

Abstract Camelina [ Camelina sativa (L.) Crantz] is an oilseed crop in the Brassicaceae family that is currently being developed as a source of bioenergy and healthy fatty acids. To facilitate modern breeding efforts through marker‐assisted selection and biotechnology, we evaluated genetic variation among a worldwide collection of 222 camelina accessions. We performed whole‐genome resequencing to obtain single nucleotide polymorphism (SNP) markers and to analyze genomic diversity. We also conducted phenotypic field evaluations in two consecutive seasons for variations in key agronomic traits related to oilseed production such as seed size, oil content (OC), fatty acid composition, and flowering time. We determined the population structure of the camelina accessions using 161,301 SNPs. Further, we identified quantitative trait loci (QTL) and candidate genes controlling the above field‐evaluated traits by genome‐wide association studies (GWAS) complemented with linkage mapping using a recombinant inbred line (RIL) population. Characterization of the natural variation at the genome and phenotypic levels provides valuable resources to camelina genetic studies and crop improvement. The QTL and candidate genes should assist in breeding of advanced camelina varieties that can be integrated into the cropping systems for the production of high yield of oils of desired fatty acid composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Genomic analysis of Klebsiella aerogenes circulating in New Mexico

Klebsiella aerogenes is an opportunistic pathogen and a growing cause of healthcare-associated infections, characterized by multidrug resistance and the emergence of global high-risk clones. However, regional genomic surveillance data remain limited. Here, we sought to characterize the population structure, transmission dynamics and resistance mechanisms of clinical K. aerogenes in Albuquerque, New Mexico. We sequenced 177 clinical isolates collected between 2021 and 2023. We also developed a novel, species-specific PopPUNK database to facilitate rapid, high-resolution typing. The New Mexico K. aerogenes population was diverse but dominated by two global pandemic lineages, ST93 (47.5%) and ST4 (7.9%), which were significantly enriched for the virulence factors yersiniabactin and colibactin. Genomic evidence for recent local transmission was rare, with only four putative transmission pairs identified. The resistome was characterized by intrinsic and adaptive mutations. Nearly all isolates possessed gyrA mutations associated with decreased fluoroquinolone susceptibility. Mutations in the AmpC regulator AmpD and the outer membrane porin Omp36 were common, particularly within the dominant ST93 lineage. These mutations have been associated with increased AmpC-mediated carbapenem resistance. Our findings underscore the critical importance of genomic surveillance to monitor the transmission and evolution of adaptive resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology

Type A γ-aminobutyric acid receptors (GABA A Rs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants. However, our understanding of GABA A R pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABA A R assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABA A Rs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABA A R assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Geographic_Distribution_of_Populus_trichocarpa_Genotypes_by_DBSCAN_Cluster

Aninteractive mapshowingPopulus trichocarpaGWAS sub-population structure identified by DBSCAN clustering, which were derived from a UMAP projection of the top 8 PCs of LD-pruned pangenome SNP data. Geographic origins are searchable by genotype or river system using the search bar.

09 BIOMASS FUELS↗
DOE OSTI2023

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers

Molecular characterization of diverse germplasm can contribute to breeding programs by increasing genetic gain for sorghum [ Sorghum bicolor (L.) Moench] improvement. Identifying novel marker-trait associations and candidate genes enriches the existing genomic resources and can improve bioenergy-related traits using genomic-assisted breeding. In the current scenario, identifying the genetic loci underlying biomass and carbon partitioning is vital for ongoing efforts to maximize each carbon sink’s yield for bioenergy production. Here, we have processed a high-density genomic marker (22 466 550) data based on whole-genome sequencing (WGS) using a set of 365 accessions from the bioenergy association panel (BAP), which includes ~19.7 million (19 744 726) single nucleotide polymorphism (SNPs) and 2.7 million (~2 721 824) insertion deletions (indels). A set of high-quality filtered SNP (~5.48 million) derived markers facilitated the assessment of population structure, genetic diversity, and genome-wide association studies (GWAS) for various traits related to biomass and its composition using the BAP. The phenotypic traits for GWAS included seed color (SC), plant height (PH), days to harvest (DTH), fresh weight (FW), dry weight (DW), brix content % (BRX), neutral detergent fiber (NDF), acid detergent fiber (ADF), non-fibrous carbohydrate (NFC), and lignin content. Several novel loci and candidate genes were identified for bioenergy-related traits, and some well-characterized genes for plant height ( Dw1 and Dw2 ) and the YELLOW SEED1 locus ( Y1 ) were validated. We further performed a multi-variate adaptive shrinkage analysis to identify pleiotropic QTL, which resulted in several shared marker-trait associations among bioenergy and compositional traits. Significant marker-trait associations with pleiotropic effects can be used to develop molecular markers for trait improvement using a marker-assisted breeding approach. Significant nucleotide diversity and heterozygosity were observed between photoperiod-sensitive and insensitive individuals of the panel. This diverse bioenergy panel with genomic resources will provide an excellent opportunity for further genetic studies, including selecting parental lines for superior hybrid development to improve biomass-related traits in sorghum.

bioenergy association panel↗
NASA NTRS2009

Steady-State ALPS for Real-Valued Problems

The two objectives of this paper are to describe a steady-state version of the Age-Layered Population Structure (ALPS) Evolutionary Algorithm (EA) and to compare it against other GAs on real-valued problems. Motivation for this work comes from our previous success in demonstrating that a generational version of ALPS greatly improves search performance on a Genetic Programming problem. In making steady-state ALPS some modifications were made to the method for calculating age and the method for moving individuals up layers. To demonstrate that ALPS works well on real-valued problems we compare it against CMA-ES and Differential Evolution (DE) on five challenging, real-valued functions and on one real-world problem. While CMA-ES and DE outperform ALPS on the two unimodal test functions, ALPS is much better on the three multimodal test problems and on the real-world problem. Further examination shows that, unlike the other GAs, ALPS maintains a genotypically diverse population throughout the entire search process. These findings strongly suggest that the ALPS paradigm is better able to avoid premature convergence then the other GAs.

Hornby, Gregory S.↗
DOE OSTI2022

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

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

Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision

Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Applying cumulative effects to strategically advance large-scale ecosystem restoration

Programs restoring large terrestrial-aquatic ecosystems are expected to increase in area and number over the next decade. Factors ensuring long-term effectiveness at the program scale differ from those at the individual restoration project scale, necessitating a new synthesis. Here we contextualize hydrological, geomorphological, and biological effects of large-scale ecosystem restoration activities within a cumulative-effects paradigm. Evidence of eight modes of cumulative effects benefiting species and ecosystems was elucidated by reviewing restoration efforts in the greater Florida Everglades, Gulf Coast, lower Columbia River and estuary, Puget Sound estuary, Missouri River, northeastern coastal states, San Francisco Bay and Sacramento Delta. Additive and nonlinear cumulative effects of interacting restoration projects propagated across landscape and regional geographic scales, and throughout trophic levels, affecting population structures. Applying a cumulative-effects paradigm to planning, implementing, and evaluating large-scale restoration will avoid countervailing effects and capitalize on positive feedback, advancing evidence-based programs to recover priority species and ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A Review of Coccidioides Research, Outstanding Questions in the Field, and Contributions by Women Scientists

Abstract Purpose of Review Coccidioidomycosis is an infectious disease that gained clinical significance in the early 20th century. Many of the foundational contributions to coccidioidomycosis research, including the discovery of the fungal disease agent, Coccidioides spp., were made by women. We review recent progress in Coccidioides research and big questions remaining in the field, while highlighting some of the contributions from women. Recent Findings New molecular-based techniques provide a promising method for detecting Coccidioides, which can help determine the dominate reservoir host and ideal environmental conditions for growth. Genetic and genomic analyses have allowed an understanding of population structure, species level diversity, and evolutionary histories. We present a current, comprehensive genome list, where women contributed many of these entries. Several efforts to develop a coccidioidomycosis vaccine are underway. Summary Women continue to pioneer research on Coccidioides, including the relationships between the fungi and the environment, genetics, and clinical observations. Significant questions remain in the field of Coccidioides, including the main host reservoir, the relationships between genotypic and phenotypic variation, and the underlying cause for chronic clinical coccidioidomycosis cases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ecological connectivity and in-kind mitigation in a regulatory decision framework: A case study with an amphibian habitat specialist

Ecological connectivity is critical to the survival and long-term viability of populations but is often overlooked in regulatory frameworks. We integrated landscape-level processes into a mitigation strategy for impacts to aquatic resources on the U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) in eastern Tennessee. Wetlands on the ORR, which contain significant breeding populations of the imperiled four-toed salamander (Hemidactylium scutatum) and tubercled rein orchid (Platanthera flava var. herbiola), will be impacted by construction of an environmental waste disposal facility under the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA). Here, we used a modified Kepner-Tregoe decision analysis to select general mitigation options that balanced regulatory requirements and interest group perspectives. We emphasized habitat connectivity through models that prioritized an area's importance to natural area connectivity (centrality) and maintenance of population structure for an affected habitat specialist (four-toed salamanders). We also emphasized in-kind mitigation through the preservation and enhancement of ecologically similar resources and the translocation and establishment of a new subpopulation of four-toed salamanders elsewhere on the ORR. We ultimately released over 500 juvenile salamanders that originated from the impacted site into the chosen mitigation wetlands. By doing so under the constraints of a time-sensitive CERCLA remediation effort and exceeding its substantive requirements, this work underscores feasibility. Ecological connectivity and the conservation of species that are not afforded explicit regulatory processes can be effectively and efficiently integrated into environmental decision-making and land use planning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Prandtl number effects on extreme mixing events in forced stratified turbulence

Relatively strongly stratified turbulent flows tend to self-organise into a ‘layered anisotropic stratified turbulence’ (LAST) regime, characterised by relatively deep and well-mixed density ‘layers’ separated by relatively thin ‘interfaces’ of enhanced density gradient. Understanding the associated mixing dynamics is a central problem in geophysical fluid dynamics. It is challenging to study LAST mixing, as it is associated with Reynolds numbers $Re := UL/\nu \gg 1$ and Froude numbers $Fr :=(2{\rm \pi} U)/(L N) \ll 1$ ( $U$ and $L$ being characteristic velocity and length scales, $\nu$ the kinematic viscosity and $N$ the buoyancy frequency). Since a sufficiently large dynamic range (largely) unaffected by stratification and viscosity is required, it is also necessary for the buoyancy Reynolds number $Re_{b} := \epsilon /(\nu N^{2}) \gg 1$ , where $\epsilon$ is the (appropriately volume-averaged) turbulent kinetic energy dissipation rate. This requirement is exacerbated for oceanically relevant flows, as the Prandtl number $Pr := \nu /\kappa = {O}(10)$ in thermally stratified water (where $\kappa$ is the thermal diffusivity), thus leading (potentially) to even finer density field structures. We report here on four forced fully resolved direct numerical simulations of stratified turbulence at various Froude ( $Fr=0.5, 2$ ) and Prandtl ( $Pr=1, 7$ ) numbers forced so that $Re_{b}=50$ , with resolutions up to $30\,240 \times 30\,240 \times 3780$ . We find that, as $Pr$ increases, emergent ‘interfaces’ become finer and their contribution to bulk mixing characteristics decreases at the expense of the small-scale density structures populating the well-mixed ‘layers’. However, extreme mixing events (as quantified by significantly elevated local destruction rates of buoyancy variance $\chi _0$ ) are always preferentially found in the (statically stable) interfaces, irrespective of the value of $Pr$ .

Mechanics↗
DOE OSTI2021

Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics

Abstract The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A clearer picture of who lives in the world’s cities

A new city-level dataset examines how urban population structures have changed worldwide between 2000 and 2020. Here, the work reveals divergent age distributions, sex ratios and migration patterns across more than 10,000 cities, and it provides evidence for locally tailored urban planning.

Zimmer, Andrew [Oak Ridge National Laboratory (ORN↗
DOE OSTI2020

Interpretation of Lyman opacity measurements in JET with the ITER-like wall using a particle balance approach

Recent measurements of the Ly β /D α ratio in the JET ITER-like wall (ILW) divertor show comparatively more pronounced Ly β reabsorption relative to previous results in JET with the carbon wall (JET-C). At the outer horizontal target ion current rollover point a Ly β reabsorption rate of 60% is measured, increasing to 80% in more pronounced detachment, implying a Ly α reabsorption rate of 90%–98%. The radially resolved Ly β /D α measurements are used to constrain Lyman opacity corrections to atomic rate coefficients using the population escape factor technique in order to capture the local changes to the excited state population structure in the high Lyman opacity regions at and outboard of the outer strike point. To check the self-consistency of the Lyman opacity measurements, a detailed spectroscopic interpretation of the outer divertor particle balance is presented, in which the impact of opacity corrections to the Ly α inverse photon efficiency coefficients is assessed. A five-fold deficit in the estimated D + source rate obtained with optically thin plasma assumptions is reconciled once the opacity corrections are factored into the Ly α photon rate to ionization rate conversion. The experiment results are reproduced in EDGE2D-EIRENE density scan simulations in which an imposed ad hoc Lyman reabsorption rate is recovered spectroscopically using synthetic measurements, and a similar shortfall in the D + source rate estimates is reconciled using Lyman opacity corrected atomic data. The model limitations prevent a more detailed self-consistent analysis of the Lyman opacity impact on divertor parameters and detachment evolution, and hence motivate renewed efforts to re-establish routine exploitation of the photon transport modelling capabilities in the EIRENE code package. Lyman opacity corrections to atomic data coefficients are necessary for spectroscopic interpretation of the JET-ILW divertor plasma, with significant influence on the divertor plasma also a likely consequence of the presence of strong Ly α reabsorption. Finally, a scan of auxiliary heating powers spanning L-mode and H-mode conditions reveals a strong correlation of the measured Ly β opacity with the outer target temperature, suggesting new possibilities for using Lyman opacity measurements in establishing detachment scalings.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Natural variation and improved genome annotation of the emerging biofuel crop field pennycress ( Thlaspi arvense )

The Brassicaceae family comprises more than 3,700 species with a diversity of phenotypic characteristics, including seed oil content and composition. Recently, the global interest in Thlaspi arvense L. (pennycress) has grown as the seed oil composition makes it a suitable source for biodiesel and aviation fuel production. However, many wild traits of this species need to be domesticated to make pennycress ideal for cultivation. Molecular breeding and engineering efforts require the availability of an accurate genome sequence of the species. Here, we describe pennycress genome annotation improvements, using a combination of long- and short-read transcriptome data obtained from RNA derived from embryos of 22 accessions, in addition to public genome and gene expression information. Our analysis identified 27,213 protein-coding genes, as well as on average 6,188 biallelic SNPs. In addition, we used the identified SNPs to evaluate the population structure of our accessions. The data from this analysis support that the accession Ames 32872, originally from Armenia, is highly divergent from the other accessions, while the accessions originating from Canada and the United States cluster together. When we evaluated the likely signatures of natural selection from alternative SNPs, we found 7 candidate genes under likely recent positive selection. These genes are enriched with functions related to amino acid metabolism and lipid biosynthesis and highlight possible future targets for crop improvement efforts in pennycress.

59 BASIC BIOLOGICAL SCIENCES↗