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DOE OSTI2026

Single-cell and spatial omics in plants: from cellular atlases to regulatory mechanisms

Single-cell RNA sequencing (scRNA-seq) has transformed transcriptomic studies by enabling gene expression profiling at the resolution of individual cells within and across a broad range of tissue types, revealing cellular heterogeneity that is obscured in bulk tissue transcriptomes. Over the past decade, improvements in microfluidics and library preparation have drastically increased throughput, allowing tens of thousands of cells to be assayed in a single experiment. Although initially developed in animal systems, scRNA-seq has rapidly emerged as a powerful and widely adopted approach in plant biology. Beyond transcriptomics, the integration of single-cell data with chromatin accessibility, proteomics, metabolomics, and spatial omics is enabling a system-level understanding of plant gene regulation and cellular organization. Network-based analytical frameworks further support the reconstruction of gene regulatory networks and the interpretation of complex single-cell data. In this review, we summarize the current technological landscape of plant single-cell studies, discuss key experimental and analytical challenges, and review emerging strategies for validating single-cell discoveries. We also discuss future directions in applying single-cell technologies to woody perennials plants and bioenergy-relevant crops, emphasizing their potential to accelerate the discovery of cell type-specific regulatory mechanisms underlying growth, stress resilience, and biomass production.

Li, Miaomiao [ORNL] (ORCID:0000000321326168)↗

DOE OSTI2022

Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist

The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO 2 via beta oxidation and the oxidative Wood–Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Epithermal Neutron Resonance Analysis Using a Compact D-T Generator

Nuclear material identification and isotopic composition analysis are important capabilities for safeguards and the verification of nuclear arms control and nonproliferation treaties. Epithermal neutron resonance imaging has been proposed for spent fuel assay measurements, and the development of a mobile neutron imaging system could provide such a tool for on-site applications. This technique is highly sensitive to isotopes of interest for safeguards applications (e.g. 235,238 U, 238,239,240 Pu) and yields unique transmission spectra for a target containing actinides and some mid- and high-Z elements. Paired with a position-sensitive neutron detector, such a system could provide spatial information of the target isotopic composition. Recent progress in the development of high intensity neutron sources could make mobile epithermal neutron imaging designs increasingly feasible to serve as a tool for nuclear inspectors. In this work, Monte Carlo (MC) simulations were performed to further optimize a previous design for an epithermal neutron resonance-based analysis apparatus using a D-T portable neutron generator. Additionally, experimental work is being performed to test the feasibility of this method. The MC simulations of moderation time distributions for different moderator compositions and thicknesses were measured to provide a multi-group correction for neutron time-of-flight energy reconstruction.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Peripheral blood hematology, plasma biochemistry, and the optimization of an in vitro immune-based assay in the brown watersnake ( Nerodia taxispilota )

Reptiles represent a phylogenetic lineage that provides a unique link between ectothermic anamniotes and endothermic amniotes. Compared to mammalian and avian species, our understanding of the reptilian immune system is greatly lacking. This gap in knowledge is largely due to an absence of established immune-based assays or specific reagents for these species. In the present study, brown watersnakes (Nerodia taxispilota) were live-captured in the wild, sexed, weighed, measured, bled via the caudal vein and released. At 24 hr post-collection, peripheral blood leukocytes were enriched and evaluated with an established mammalian in-vitro lymphocyte proliferation assay. Snake peripheral blood leukocyte enrichment yielded > 90% lymphocytes with viabilities averaging 81.5%. Baseline physiologic data for N. taxispilota, including hematology and total solids, leukocyte differentials, cell recovery and plasma biochemistry, were also collected. Cells cultured with Concanavalin A exhibited significantly increased proliferation at both 72 and 96 hr. Furthermore, these preliminary results show that enriched peripheral blood from wild-caught N. taxispilota provides a sufficient yield of leukocytes that can be cultured and functionally evaluated using a standard mammalian in-vitro immune-based assay.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Mitochondrial Effects in the Liver of C57BL/6 Mice by Low Dose, High Energy, High Charge Irradiation

Galactic cosmic rays are primarily composed of protons (85%), helium (14%), and high charge/high energy ions (HZEs) such as 56 Fe, 28 Si, and 16 O. HZE exposure is a major risk factor for astronauts during deep-space travel due to the possibility of HZE-induced cancer. A systems biology integrated omics approach encompassing transcriptomics, proteomics, lipidomics, and functional biochemical assays was used to identify microenvironmental changes induced by HZE exposure. C57BL/6 mice were placed into six treatment groups and received the following irradiation treatments: 600 MeV/n 56 Fe (0.2 Gy), 1 GeV/n 16 O (0.2 Gy), 350 MeV/n 28 Si (0.2 Gy), 137 Cs (1.0 Gy) gamma rays, 137 Cs (3.0 Gy) gamma rays, and sham irradiation. Left liver lobes were collected at 30, 60, 120, 270, and 360 days post-irradiation. Analysis of transcriptomic and proteomic data utilizing ingenuity pathway analysis identified multiple pathways involved in mitochondrial function that were altered after HZE irradiation. Lipids also exhibited changes that were linked to mitochondrial function. Molecular assays for mitochondrial Complex I activity showed significant decreases in activity after HZE exposure. HZE-induced mitochondrial dysfunction suggests an increased risk for deep space travel. Microenvironmental and pathway analysis as performed in this research identified possible targets for countermeasures to mitigate risk.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Optimal scheduling for profit maximization of energy storage merchants considering market impact based on dynamic programming

This paper analyzes how electricity merchants' market impact affects merchants' profit. Energy storage has long been studied for its role in maximizing profit, and merchant decisions are assumed to have no impact on market prices. However, the trading decisions of large-scale energy storage merchants (e.g., pumped storage hydro) will affect the market prices. This paper employs dynamic programming theory to investigate merchants' optimal economic dispatch considering the market impact and physical characteristics of storage systems. Our findings show that the State-of-Charge (SOC) based analytical solution significantly facilitates energy storage merchants' decision-making. The SOC range is segmented into three regions by two optimal SOC reference points, which depend on the available energy in storage, given prices, and market impact. By comparing the current storage SOC with the reference points, the merchant can get the corresponding optimal actions. We analytically show that if the merchant neglects the market impact on the power market, she will exaggerate her expected profit when the price-taker and price-maker merchants have the same generating and pumping upper limits offered to Independent System Operators (ISOs). Furthermore, the profit-maximizing merchant must, therefore, assay to balance the trade-off correctly between the intensity of market impact and the dispatched power. Our findings are verified by numerical simulation, and results demonstrate the ramifications for electricity merchants in energy arbitrage decisions.

25 ENERGY STORAGE↗

DOE OSTI2020

ExINP-ENA Ice-Nucleating Particle Concentrations - CRAFT

This data set comprises cumulative ambient ice-nucleating particle (INP) concentrations measured at the U.S. Department of Energy's Atmospheric Radiation Measurement (ARM) Eastern North Atlantic (ENA) observatory on Graciosa Island, Azores (39.0916° N, 28.0257° W). Our INP data were generated using a combination of online instruments, the Portable Ice Nucleation Experiment chamber (PINE), and an offline assay instrument, the West Texas Cryogenic Refrigerator Applied to Freezing Test system (WT-CRAFT), for aerosol particle samples collected on polycarbonate filters (with 0.2-micron diameter pores).

47-mm Nuclepore filter sampler, West Texas Cryogen↗

DOE OSTI2020

ExINP-ENA Ice-Nucleating Particle Concentrations - PINE

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus

Abstract Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.

Biochemistry & Molecular Biology↗

DOE OSTI2020

A Preliminary Radiological Risk Assessment Model for Disposition of Remote-Handled Transuranic Wastes at Los Alamos National Laboratory Area G - 20116

The U.S. Department of Energy (DOE) operates a low-level radioactive waste (LLW) disposal site at Material Disposal Area G, in Los Alamos, New Mexico, USA. Area G has been the primary LLW disposal site for Los Alamos National Laboratory (LANL) since the 1960's. In addition to LLW, Area G is host to a variety of other wastes, the disposition of which must be determined before closure of the site. A probabilistic Radiological Risk Assessment (RRA) for Area G is used in order to support decision making regarding some wastes that are not addressed in the extant Area G Performance Assessment (PA) and Composite Analysis (CA). Between 1979 and 1987, 33 special shafts were augered into the Bandelier Tuff at Area G. This volcanic tuff is present across Pajarito Plateau on the eastern slopes of the Jemez Mountains, and varies widely in its consistency, from weakly indurated non-welded layers to welded layers that uphold the mesa cliffs of the Plateau. These mesas are home to LANL, Area G, and the townsites of Los Alamos and White Rock, with residences about 1400 m from Area G. The 33 Shafts were lined with steel casing, and contain remote-handled (RH) transuranic wastes (TRU) resulting from experiments and analysis performed in special glove boxes at the Chemistry and Metallurgy Research (CMR) facility at LANL. Some of these wastes originated as used nuclear fuel. The purpose of the Area G RRA is to evaluate the potential future risk to humans and the environment from the RH TRU in the 33 Shafts in the context of the risk associated with the surrounding wastes at Area G. The analysis is responsive to expectations outlined in DOE Order 458.1, Radiation Protection of the Public and the Environment, and is informed by the Manual and Guidance accompanying DOE O 435.1, Radioactive Waste Management. Because the waste meets the definition of TRU, the regulatory context necessarily takes into consideration the regulation governing the disposal of TRU from the U.S. Environmental Protection Agency (EPA): 40 CFR 191, Environmental Radiation Protection Standards for Management and Disposal of Spent Nuclear Fuel, High-Level and Transuranic Radioactive Wastes. Given the broader regulatory context for the RRA, the analysis is subject to different assumptions from those made in the existing DOE O 435.1 PA and CA, such as allowing for future occupation of the site. The analysis begins with a comprehensive evaluation of features, events, processes, and exposure scenarios (FEPS) for Area G and the wastes it contains. These FEPSs are screened to eliminate from further consideration those of extremely low probability and/or consequence, and a conceptual site model (CSM) is subsequently developed. The scope and structure of the Area G RRA Model is informed by this CSM, and the Area G RRA Model is developed using the GoldSim systems analysis modeling platform. This paper presents the initial version of a defensible, transparent, and reasonably realistic model, which is based on the state of knowledge of the wastes, the site, and the FEPSs that govern contaminant transport from wastes into the environment and subsequent exposures to humans and other biota. Probabilistic model input distributions represent uncertainties inherent in the real and modeled systems. The results of the Area G RRA Model inform decisions regarding the disposition of the RH TRU in the 33 Shafts. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Genome-wide toxicogenomic study of the lanthanides sheds light on the selective toxicity mechanisms associated with critical materials

Significance The growing use of lanthanides in various industries has increased the potential for human exposure to large concentrations of these heavy metals throughout the life cycle of new technologies, requiring more detailed investigations into their toxicological properties. The eukaryote model organism Saccharomyces cerevisiae is ideal to apply functional toxicogenomics tools at the system level and probe fundamental cellular functions disrupted by rare-earth metals. A comprehensive mechanistic assay was conducted to evaluate toxicity across the entire lanthanide series and provide information about which toxicological mechanisms may be shared by the different metals. We identified distinct characteristic behaviors between early and middle/late lanthanides, highlighting the powerful discrimination capabilities of natural systems and pointing to detailed mechanistic pathways associated with lanthanide exposure.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗

DOE OSTI2024

Neutron resonance transmission analysis prototype system for thorium fuel cycle safeguards

Emerging thorium-based reactor designs and fuel cycles present challenges to traditional non-destructive assay techniques used in international safeguards. Specifically, assaying the masses of 233 U and 235 U when they are present together in samples with high gamma ray backgrounds is difficult because of similar passive neutron signatures and relatively weak gamma-ray emissions of 233 U. The Pacific Northwest National Laboratory (PNNL) and the Massachusetts Institute of Technology (MIT) are developing a compact neutron resonance transmission analysis (NRTA) system as one potential solution to these challenges. The NRTA technique provides isotopic information for a sample via neutron time-of-flight (TOF) measurements that exploit a sample’s epithermal neutron resonance cross-sections. A recently developed portable NRTA system uses a commercially available, pulsed deuterium-tritium neutron generator with a ~2 m flight path and a GS20 lithium glass scintillator detector. Finally, this paper describes the prototype NRTA system design, a refined radiation transport model of the system, preliminary measurements with thorium and uranium sources, and demonstration of a quantitative isotopic estimation algorithm.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

INL Report: Multiphysics Modeling and Simulation of Deimos, an Advanced Reactor Experiment

When designing a novel reactor, nuclear experiments are essential to validate the predictive capability of modeling/simulation tools and to justify the investment of a full-scale prototype. Being able to accurately predict temperature reactivity coefficients is of high importance to reactor designers as it impacts the safety and performance of the system. Deimos is a proposed graphite-moderated, beryllium-reflected, high assay low-enriched uranium (HALEU) tri-structural isotropic (TRISO) fueled experiment for NCERC. Deimos is a valuable experiment for validating the predictive performance of modeling and simulation tools since it comprises a relatively thermal energy spectrum with 84% thermal neutrons causing fission, 15% epithermal neutrons causing fission, and 1% fast neutrons causing fission. Additionally, by electrically heating the experiment, reactivity can be validated at various temperatures. Deimos will serve as a testbed for future advanced reactor concepts.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Protoplast-Based Transient Expression and Gene Editing in Shrub Willow ( Salix purpurea L .)

Shrub willows (Salix section Vetrix) are grown as a bioenergy crop in multiple countries and as ornamentals across the northern hemisphere. To facilitate the breeding and genetic advancement of shrub willow, there is a strong interest in the characterization and functional validation of genes involved in plant growth and biomass production. While protocols for shoot regeneration in tissue culture and production of stably transformed lines have greatly advanced this research in the closely related genus Populus, a lack of efficient methods for regeneration and transformation has stymied similar advancements in willow functional genomics. Moreover, transient expression assays in willow have been limited to callus tissue and hairy root systems. Here we report an efficient method for protoplast isolation from S. purpurea leaf tissue, along with transient overexpression and CRISPR-Cas9 mediated mutations. This is the first such report of transient gene expression in Salix protoplasts as well as the first application of CRISPR technology in this genus. These new capabilities pave the way for future functional genomics studies in this important bioenergy and ornamental crop.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Extended Enrichment Accident Tolerant LWR Fuel Isotopic and Lattice Parameter Trends

Commercial light water reactor (LWR) operators and fuel vendors in the United States (US) are pursuing changes to the reactor fuel that include increased enrichment and accident-tolerant fuel (ATF) designs. Enrichments under consideration are between 5 wt % and 10 wt % 235 U, which are a subset of high-assay low-enriched uranium fuels. ATF features are designed to improve fuel system performance under accident conditions. With increased enrichment, fuel cycle economics can be improved if fuel can be licensed for higher burnup (HBU) than typical current limits (e.g., 62 GWd/MTU maximum fuel pin).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Fixed-Energy Response-Function Analysis with Multi-Efficiency (FRAM) Software, Version 6

Researchers at Los Alamos National Laboratory have developed FixedEnergy Response- Function Analysis with Multiple Efficiency (FRAM), a powerful software tool for gamma-ray spectrometry isotopic analysis. This tool leverages Los Alamos expertise in nuclear safeguards, radiation detection systems, and related analysis techniques. A household name in the non-destructive assay community for over two decades, FRAM determines a special nuclear material source's isotopic composition by analyzing gamma-ray spectra. Los Alamos researchers have released the latest version of FRAM that incorporates several updates to the 2013 major release of FRAM, Version 5.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Pros and Cons Analysis of HALEU Utilization in Example Fuel Cycles

The Systems Analysis and Integration campaign assessed the pros and cons of high-assay low-enriched uranium (HALEU) utilization in advanced reactors and associated fuel cycles. The assessment was done for three example fuel cycles at equilibrium states: once-through, limited recycle, and continuous recycle (CR) starting with HALEU. Front- and back-end fuel cycle parameters and the Levelized Cost of Fuel (LCF), which is the Levelized Cost of Electricity excluding reactor cost, of the three example fuel cycles were calculated using a single Analysis Example Reactor. The pros and cons of HALEU utilization were assessed by normalizing the fuel cycle parameters and LCF to a unit of electricity generation (GWe-year) and comparing them with a Basis of Comparison. In this study, a sodium-cooled reactor with sodium-bonded metallic fuel having a burnup of ~100 GWd/t was used as the Analysis Example Reactor because its technology readiness level is high, and the burnup and fuel enrichment are in the middle of those ranges of advanced reactor concepts that are under development. The current once-through Light Water Reactors (OT-LWRs) with <5% low-enriched uranium and 50 GWd/t burnup were used as the Basis of Comparison. In addition, a series of sensitivity analyses was conducted by varying burnup, enrichment, fuel forms, and reactor types to capture the design variations in two once-through Advanced Reactor Demonstration Program (ARDP) reactors, Natrium with sodium-free metallic fuel having a burnup of ~150 GW/t and Xe-100 with Tristructural-Isotropic (TRISO) pebble fuel having a burnup of ~168 GWd/t.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗