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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Evolutionary and functional relationships between plant and microbial C 1 metabolism in terrestrial ecosystems

One-carbon (C 1 ) metabolism, centered on the universal methyl donor S-adenosyl methionine (SAM), plays critical roles in biosynthesis, redox regulation, and stress responses across plants and microbes. A recently proposed photosynthetic C 1 pathway links SAM methyl groups directly to RuBisCO-mediated CO 2 assimilation and integrates with nitrogen and sulfur metabolism. Light-dependent SAM synthesis may regulate the methylation of biopolymers and specialized metabolites and help mitigate photorespiratory stress under elevated temperature and drought. Phylogenetic analysis of two core enzymes suggests evolutionary continuity from methylotrophic microbes to land plants, supporting microbial origins via endosymbiotic gene transfer. Beyond intracellular roles, C 1 metabolism drives biosphere–atmosphere exchange via gases such as methane, methanol, formic acid, and formaldehyde, and numerous specialized volatiles synthesized through SAM methylation. S-methylmethionine, a mobile C 1 metabolite, may mediate phloem transport of reduced sulfur, nitrogen, and methyl groups, linking above- and belowground C 1 cycling in plants. Advances in real-time gas sensing now allow the high-frequency quantification of C 1 fluxes from leaves, stems, and soils, highlighting C 1 metabolism as a critical and underrecognized component of terrestrial carbon and nutrient cycling. Given its microbial ancestry and the production of diverse volatile biosignatures, C 1 metabolism may also offer unique insights into life's origins and biosignature detection on exoplanets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA

We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling—particularly methane-cycling—microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.

58 GEOSCIENCES↗
DOE OSTI2025

Non-stoichiometry Governs the Pathway from Amorphous to Crystalline Calcium Carbonate

The controlled crystallization of calcium carbonate underlies the elaborate architectures of marine corals, the design of biomimetic materials, and the global carbon cycle. Despite its ubiquity, the chemical mechanisms that govern the crystallization of calcium carbonate from its amorphous precursor, amorphous calcium carbonate (ACC), remain elusive, largely due to the difficulty in resolving the structure and chemistry of this transient amorphous state. Here, we use time-lapse photography, image analysis, spatially resolved pH determination, in situ synchrotron pair distribution function (PDF) analysis, and dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance (NMR) spectroscopy to reveal pervasive compositional variability in ACC that underpins its metastability and crystallization. By evaluating the kinetics of the amorphous-to-crystalline transition across different solution chemistries, we demonstrate that ACC is non-stoichiometric and CO 3 -deficient. Counterions from the precursor (e.g., NO 3 - from Ca(NO 3 ) 2 ) substitute into the ACC network, displacing CO 3 ions and mediating both ACC stability and transformation. Crystallization proceeds through refinement of the stoichiometry toward CaCO 3 and uptake of free CO 3 2- anions. Furthermore, these findings are consistent across a wide range of concentrations and different carbonate sources, explaining the diverse behaviors observed for ACC and providing a chemical framework for controlling calcium carbonate crystallization.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Vegetation-induced asymmetric diurnal land surface temperatures changes across global climate zones

Unprecedented global vegetation greening during past decades is well known to affect annual and seasonal land surface temperatures (LST). However, the impact of observed vegetation cover change on diurnal LST across global climatic zones is not well understood. In this study, using global climatic time-series datasets, we investigated the long-term growing season daytime and nighttime LST changes globally and explored associated dominant contributors including vegetation and climate factors including air temperature, precipitation, and solar radiation. Results revealed asymmetric growing season mean daytime and nighttime LST warming (0.16 °C/10a and 0.30 °C/10a, respectively) globally from 2003 to 2020, as a result, the diurnal LST range (DLSTR) declined at 0.14 °C/10a. The sensitivity analysis indicated the LST response to changes in LAI, precipitation, and SSRD mainly concentrated during daytime instead of nighttime, however, which showed comparable sensitivities for air temperature. Combining the sensitivities results and the observed LAI and climate trends, we found rising air temperature contributes to 0.24 ± 0.11 °C/10a global daytime LST warming and 0.16 ± 0.07 °C/10a nighttime LST warming, turns to be the dominant contributor to the LST changes. Increased LAI cooled global daytime LST (–0.068 ± 0.096 °C/10a) while warmed nighttime LST (0.064 ± 0.046 °C/10a); hence LAI dominates declines in DLSTR trends (–0.12 ± 0.08 °C/10a), despite some daynight process variations across climate zones. In Boreal regions, reduced DLSTR was due to nighttime warming from LAI increases. In other climatic zones, daytime cooling, and DLSTR decline, was induced by increased LAI. Biophysically, the pathway from air temperature heats the surface through sensible heat and increased downward longwave radiation during day and night, while the pathway from LAI cools the surface by enhancing energy redistribution into latent heat rather than sensible heat during the daytime. These empirical findings of diverse asymmetric responses could help calibrate and improve biophysical models of diurnal surface temperature feedback in response to vegetation cover changes in different climate zones.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2012

Multi-Factor Impact Analysis of Agricultural Production in Bangladesh with Climate Change

Diverse vulnerabilities of Bangladesh's agricultural sector in 16 sub-regions are assessed using experiments designed to investigate climate impact factors in isolation and in combination. Climate information from a suite of global climate models (GCMs) is used to drive models assessing the agricultural impact of changes in temperature, precipitation, carbon dioxide concentrations, river floods, and sea level rise for the 2040-2069 period in comparison to a historical baseline. Using the multi-factor impacts analysis framework developed in Yu et al. (2010), this study provides new sub-regional vulnerability analyses and quantifies key uncertainties in climate and production. Rice (aman, boro, and aus seasons) and wheat production are simulated in each sub-region using the biophysical Crop Environment REsource Synthesis (CERES) models. These simulations are then combined with the MIKE BASIN hydrologic model for river floods in the Ganges-Brahmaputra-Meghna (GBM) Basins, and the MIKE21Two-Dimensional Estuary Model to determine coastal inundation under conditions of higher mean sea level. The impacts of each factor depend on GCM configurations, emissions pathways, sub-regions, and particular seasons and crops. Temperature increases generally reduce production across all scenarios. Precipitation changes can have either a positive or a negative impact, with a high degree of uncertainty across GCMs. Carbon dioxide impacts on crop production are positive and depend on the emissions pathway. Increasing river flood areas reduce production in affected sub-regions. Precipitation uncertainties from different GCMs and emissions scenarios are reduced when integrated across the large GBM Basins' hydrology. Agriculture in Southern Bangladesh is severely affected by sea level rise even when cyclonic surges are not fully considered, with impacts increasing under the higher emissions scenario.

Ruane, Alex C.↗
DOE OSTI2025

Carbon-conserving bioproduction of malate in an E. coli -based cell-free system

Formate, a biologically accessible form of CO 2 , has attracted interest as a renewable feedstock for bioproduction. However, approaches are needed to investigate efficient routes for biological formate assimilation due to its toxicity and limited utilization by microorganisms. Cell-free systems hold promise due to their potential for efficient use of carbon and energy sources and compatibility with diverse feedstocks. However, bioproduction using purified cell-free systems is limited by costly enzyme purification, whereas lysate-based systems must overcome loss of flux to background reactions in the cell extract. Here, we engineer an E. coli-based system for an eight-enzyme pathway from DNA and incorporate strategies to regenerate cofactors and minimize loss of flux through background reactions. We produce the industrial di-acid malate from glycine, bicarbonate, and formate by engineering the carbon-conserving reductive TCA and formate assimilation pathways. We show that in situ regeneration of NADH drives metabolic flux towards malate, improving titer by 15-fold. Background reactions can also be reduced 6-fold by diluting the lysate following expression and introducing chemical inhibitors of competing reactions. Together, these results establish a carbon-conserving, lysate-based cell-free platform for malate production, producing 64 μM malate after 8 h. This system conserves 43 % of carbon otherwise lost as CO 2 through the TCA cycle and incorporates 0.13 mol CO 2 equivalents/mol glycine fed. Finally, techno-economic analysis of cell-free malate production from formate revealed that the high cost of lysate is a key challenge to the economic feasibility of the process, even assuming efficient cofactor recycling. This work demonstrates the capabilities of cell-free expression systems for both the prototyping of carbon-conserving pathways and the sustainable bioproduction of platform chemicals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Low-Energy Physics in Neutrino LArTPCs

In this white paper, we outline some of the scientific opportunities and challenges related to detection and reconstruction of low-energy (less than 100 MeV) signatures in liquid argon time-projection chamber (LArTPC) detectors. Key takeaways are summarized as follows. 1) LArTPCs have unique sensitivity to a range of physics and astrophysics signatures via detection of event features at and below the few tens of MeV range. 2) Low-energy signatures are an integral part of GeV-scale accelerator neutrino interaction final states, and their reconstruction can enhance the oscillation physics sensitivities of LArTPC experiments. 3) BSM signals from accelerator and natural sources also generate diverse signatures in the low-energy range, and reconstruction of these signatures can increase the breadth of BSM scenarios accessible in LArTPC-based searches. 4) Neutrino interaction cross sections and other nuclear physics processes in argon relevant to sub-hundred-MeV LArTPC signatures are poorly understood. Improved theory and experimental measurements are needed. Pion decay-at-rest sources and charged particle and neutron test beams are ideal facilities for experimentally improving this understanding. 5) There are specific calibration needs in the low-energy range, as well as specific needs for control and understanding of radiological and cosmogenic backgrounds. 6) Novel ideas for future LArTPC technology that enhance low-energy capabilities should be explored. These include novel charge enhancement and readout systems, enhanced photon detection, low radioactivity argon, and xenon doping. 7) Low-energy signatures, whether steady-state or part of a supernova burst or larger GeV-scale event topology, have specific triggering, DAQ and reconstruction requirements that must be addressed outside the scope of conventional GeV-scale data collection and analysis pathways.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Design methodologies and engineering applications for ecosystem biomimicry: an interdisciplinary review spanning cyber, physical, and cyber-physical systems

Abstract Ecosystem biomimicry is a promising pathway for sustainable development. However, while typical form- and process-level biomimicry is prevalent, system-level ecosystem biomimicry remains a nascent practice in numerous engineering fields. This critical review takes an interdisciplinary approach to synthesize trends across case studies, evaluate design methodologies, and identify future opportunities when applying ecosystem biomimicry to engineering practices, including cyber systems (CS), physical systems (PS), and cyber-physical systems (CPS). After systematically sourcing publications from major databases, the papers were first analyzed at a meta level for their bibliographic context and for statistical correlations among categorical variables. Then, we investigated deeper into the engineering applications and design methodologies. Results indicate that CPS most frequently mimic organisms and ecosystems, while CS and PS frequently mimic populations-communities and molecules-tissues-organ systems, respectively (statistically highly significant). An indirect approach is most often used for mimicry at organizational levels from populations to ecosystems, while a direct approach frequently suits levels from molecules to organisms (highly significant). Dominant themes across engineering applications include symbiotic organism search algorithms for CS and ecological network analysis for CPS, while PS are highly diverse. For design methodologies, this work summarizes and details ten well-documented biomimetic process models among literature, which addresses an outdated concern for a lack of systematic methods for ecosystem biomimicry. In addition to the Biomimetics Standard ISO 18458, these methods include the Natural Step and Techno-Ecological Synergy framework, among others. Further, the analyses revealed future opportunities from less utilized design methods (e.g. interdisciplinary teams tackling indirect, ecosystem-level projects) to well-established engineering concepts ready for technological advancement (e.g. implementing membrane computing for physical applications). For future studies, this review provides a comprehensive reference for ecosystem biomimetic design practices and application opportunities across multiple engineering domains.

42 ENGINEERING↗
DOE OSTI2023

Coordination-Dependent Chemical Reactivity of TFSI Anions at a Mg Metal Interface

Charge transfer across the electrode–electrolyte interface is a highly complex and convoluted process involving diverse solvated species with varying structures and compositions. Despite recent advances in in situ and operando interfacial analysis, molecular specific reactivity of solvated species is inaccessible due to a lack of precise control over the interfacial constituents and/or an unclear understanding of their spectroscopic fingerprints. However, such molecular-specific understanding is critical to the rational design of energy-efficient solid–electrolyte interphase layers. We have employed ion soft landing, a versatile and highly controlled method, to prepare well-defined interfaces assembled with selected ions, either as solvated species or as bare ions, with distinguishing molecular precision. Equipped with precise control over interfacial composition, we employed in situ multimodal spectroscopic characterization to unravel the molecular specific reactivity of Mg solvated species comprising (i.e., bis(trifluoromethanesulfonyl)imide, TFSI – ) anions and solvent molecules (i.e., dimethoxyethane, DME/G1) on a Mg metal surface relevant to multivalent Mg batteries. In situ multimodal spectroscopic characterization revealed higher reactivity of the undercoordinated solvated species [Mg-TFSI-G1] + compared to the fully coordinated [Mg-TFSI-(G1) 2 ] + species or even the bare TFSI – . These results were corroborated by the computed reaction pathways and energy barriers for decomposition of the TFSI – within Mg solvated species relative to bare TFSI – . Finally, we evaluated the TFSI reactivity under electrochemical conditions using Mg(TFSI) 2 –DME-based phase-separated electrolytes representing different solvated constituents. Based on our multimodal study, we report a detailed understanding of TFSI – decomposition processes as part of coordinated solvated species at a Mg-metal anode that will aid the rational design of improved sustainable electrochemical energy technologies.

25 ENERGY STORAGE↗
DOE OSTI2024

GCAM–GLORY v1.0: representing global reservoir water storage in a multi-sector human–Earth system model

Abstract. Reservoirs play a significant role in modifying the spatiotemporal availability of surface water to meet multi-sector human demands, despite representing a relatively small fraction of the global water budget. Yet the integrated modeling frameworks that explore the interactions among climate, land, energy, water, and socioeconomic systems at a global scale often contain limited representations of water storage dynamics that incorporate feedbacks from other systems. In this study, we implement a representation of water storage in the Global Change Analysis Model (GCAM) to enable the exploration of the future role (e.g., expansion) of reservoir water storage globally in meeting demands for, and evolving in response to interactions with, the climate, land, and energy systems. GCAM represents 235 global water basins, operates at 5-year time steps, and uses supply curves to capture economic competition among renewable water (now including reservoirs), non-renewable groundwater, and desalination. Our approach consists of developing the GLObal Reservoir Yield (GLORY) model, which uses a linear programming (LP)-based optimization algorithm and dynamically linking GLORY with GCAM. The new coupled GCAM–GLORY approach improves the representation of reservoir water storage in GCAM in several ways. First, the GLORY model identifies the cost of supplying increasing levels of water supply from reservoir storage by considering regional physical and economic factors, such as evolving monthly reservoir inflows and demands, and the leveled cost of constructing additional reservoir storage capacity. Second, by passing those costs to GCAM, GLORY enables the exploration of future regional reservoir expansion pathways and their response to climate and socioeconomic drivers. To guide the model toward reasonable reservoir expansion pathways, GLORY applies a diverse array of feasibility constraints related to protected land, population, water sources, and cropland. Finally, the GLORY–GCAM feedback loop allows evolving water demands from GCAM to inform GLORY, resulting in an updated supply curve at each time step, thus enabling GCAM to establish a more meaningful economic value of water. This study improves our understanding of the sensitivity of reservoir water supply to multiple physical and economic dimensions, such as sub-annual variations in climate conditions and human water demands, especially for basins experiencing socioeconomic droughts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A Pathway Analysis Framework for Evaluating the Economic and Environmental Viability of Biomass-Based Plastic Production

Plastic production from fossil feedstocks (e.g., naphtha, coal, and natural gas) is not sustainable and causes known environmental impacts such as global warming. A possible solution is to shift production pathways to use biomass, which is a sustainable feedstock that can sequester atmospheric carbon dioxide. This study presents an optimization-based pathway analysis framework for evaluating the carbon footprints of the production of mainstream plastics from biomass and fossil feedstocks. We use the modeling framework to quickly navigate complex interdependencies that exist between the production pathways of different plastics and to determine pathways of minimum production cost under a range of carbon pricing scenarios. The framework interprets carbon prices as an exogenous taxation scheme or an endogenous negative value perceived by producers. The proposed approach reveals the biomass feedstock quantities needed to displace fossil counterparts and the plastics and technologies that should be prioritized. The framework can also be used for evaluating system-wide trade-offs between production costs and carbon footprints that arise from pathway interdependencies. We also evaluate hidden environmental impacts associated with the large-scale use of biomass as a feedstock, such as land use and water eutrophication that results from a significant increase in fertilizer use. Therefore, it is important to highlight that there are trade-offs between decarbonization and other environmental issues. Here, the proposed framework provides an integrative platform for basic techno-economic and life-cycle data that can be used for analyzing diverse scenarios and determining necessary technology targets (e.g., yields, footprints, and costs) to achieve required levels of decarbonization.

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

Improved Biofuel Production through Discovery and Engineering of Terpene Metabolism in Switchgrass

Project Objectives - Of the myriad specialized metabolites that plants deploy to adapt to environmental challenges, terpenes form the largest group. In many major crops, unique terpene blends serve as key stress defenses that directly impact plant fitness and yield. In addition, terpenes, such as bisabolene and pinene, are used for producing renewable biofuels. Essential to advancing a broader use of terpenes for biofuel feedstock engineering is a system-wide knowledge of the diverse biosynthetic machinery and defensive potential of often species-specific terpene blends. The proposed project would merge genome-wide enzyme discovery with comparative –omics, protein structural and plant microbiome studies to define the biosynthesis and stress-defensive functions of the switchgrass (Panicum virgatum) terpene network. These insights would be combined with developing and applying non-transgenic genome editing tools to design plants with desirable terpene blends for higher productivity and biofuel production on marginal lands. As a dedicated lignocellulosic feedstock for U.S. biofuel production with high net energy yield, stress tolerance, and available genome resources, switchgrass is well-suited for devising new avenues for biofuel production. Project Description – The diversity of plant terpene defenses is governed by species-specific families of terpene synthase (TPS) and cytochrome P450 monooxygenase (P450) enzymes. Mining of the switchgrass genome (genotype Alamo) identified ~100 TPS and P450 candidate genes, and combinatorial biochemical analysis of synthesized TPSs and P450s revealed more than a dozen enzymes with common and novel activities. In addition, several identified terpene metabolites and the corresponding transcripts were up-regulated in response to abiotic stressors. These findings demonstrate a unique switchgrass terpene network with probable importance to abiotic stress tolerance, thus providing a large chemical portfolio for optimizing crop resistance, yield, and biofuel composition. Leveraging these preliminary data, we propose to generate a genome-wide map of the switchgrass terpene metabolic network through multi-gene co-expression analyses that allow the efficient cross-validation of TPS and P450 functions. Key enzymes would further be applied to structure-function studies via X-ray protein crystallography, homology modeling and site-directed mutagenesis to gain mechanistic insight into the catalytic specificity of switchgrass terpene metabolism and provide gene and amino acid targets for genome editing. In tandem with terpene pathway discovery, system-wide metabolomics, transcriptomics and proteomics studies in switchgrass accessions of contrasting drought tolerance would define the role of switchgrass terpene metabolism in conferring abiotic stress resilience. Metabolic changes would be assessed in a combined approach of targeted (terpenes) and untargeted metabolite profiling using a high-resolution LC-MS/MS approach, differential gene expression analyses through multiplexed Illumina RNA sequencing, and quantitative analysis of high-priority pathway enzymes using multiple reaction monitoring (MRM). Drawing on these insights, knock-down/out mutants of stress-associated pathway nodes would be generated by optimizing transient virus-induced gene silencing (VIGS) and CRISPR/Cas9 systems under control of the Tobacco Rattle Virus (TRV). The resulting mutant lines would then be analyzed for stress susceptibility and the impact on the root microbiome to define gene functions in planta. Knowledge of terpene pathways, enzyme mechanisms and bioactivities would be applied to enhance switchgrass stress resilience and to tailor-make terpene blends for biofuel production. Here, TRV-enabled CRISPR/Cas9 genome editing, including allele-specific knock-out of redundant genes, engineering of enzyme specificity via structure-guided point mutations, and overexpression of terpene genes relevant to stress-protection or biofuel production, would be used to increase metabolic flux toward desired pathways. Broader Impacts - Integrating the system-wide discovery, mechanistic analysis and non-transgenic genome engineering of the switchgrass terpene network aligns the required steps to unlock the chemical potential of this important metabolite class to generate crops that are more resistant to stress and provide advanced biofuel production in light of rising climate pressures as foreseeable challenges for bioenergy crop cultivation. The proposed project would further offer interdisciplinary student training through active involvement in the project and integration of research concepts and outcomes into newly-developed graduate and undergraduate courses on Plant Biotechnology.

09 BIOMASS FUELS↗
DOE OSTI2024

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04

Algae are a broad class of photosynthetic eukaryotes that are phylogenetically and physiologically diverse. Most of the phylogenetic diversity has been inferred from 18S rDNA sequencing since there are only a few complete genomes available in public databases. Here we use ultra-long-read Nanopore sequencing to determine a gapless, telomere-to-telomere complete genome sequence of Chlorella sp. SLA-04, previously described as Chlorella sorokiniana SLA-04. Chlorella sp. SLA-04 is a green alga that grows to high cell density in a wide variety of environments - high and neutral pH, high and low alkalinity, and high and low salinity. SLA-04's ability to grow in high pH and high alkalinity media without external CO 2 supply is favorable for large-scale algal biomass production. Phylogenetic analysis performed using ribosomal DNA and conserved protein sequences consistently reveal that Chlorella sp. SLA-04 forms a distinct lineage from other strains of Chlorella sorokiniana. We complement traditional genome annotation methods with high throughput structural predictions and demonstrate that this approach expands functional prediction of the SLA-04 proteome. Genomic analysis of the SLA-04 genome identifies the genes capable of utilizing TCA cycle intermediates to replenish cytosolic acetyl-CoA pools for lipid production. We also identify a complete metabolic pathway for sphingolipid anabolism that may allow SLA-04 to readily adapt to changing environmental conditions and facilitate robust cultivation in mass production systems. Altogether, this work clarifies the phylogeny of Chlorella sp. SLA-04 within Trebouxiophyceae and demonstrates how structural predictions can be used to improve annotation beyond sequencebased methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Achieving 50% Energy Savings in Chicago Homes: A Case Study for Advancing Equity and Climate Goals

Since 2019, the National Renewable Energy Laboratory (NREL) and Elevate have collaborated to identify pathways to deep energy retrofits in Chicago's housing stock, document equity implications and co-benefits of this transition, and validate the findings by implementing retrofits in real Chicago homes. This document summarizes our analysis process to model advanced retrofit packages that lead to greater than 50% energy savings in Chicago homes. Based on these findings, we have also developed a roadmap with the City to guide implementation, and are deploying the recommended retrofit packages in real Chicago homes to realize these energy savings. This work was developed in collaboration with two key stakeholders - the City of Chicago and Commonwealth Edison (ComEd) - and funded by the U.S. Department of Energy (DOE). NREL's Residential Buildings team maintains the best-in-class ResStock™ energy model of the U.S. residential building stock. For this work, we calibrated ResStock to Chicago's unique local housing stock to accurately simulate energy use in Chicago homes both for current conditions and with various retrofit scenarios. We simulated a wide range of potential building retrofits covering all aspects of residential energy use and then grouped these into packages based on energy and utility bill savings. ResStock can model diverse building types and housing characteristics, so we're able to observe the range of outcomes that might occur when these upgrades are deployed across the entire housing stock. We can then estimate potential energy savings from an advanced retrofit program on Chicago's housing stock by comparing the modeled energy use before versus after a retrofit. This novel version of ResStock, calibrated to Chicago with data from Elevate, can help City officials, ComEd, and other partners plan for community-scale decarbonization via residential retrofits. Specifically, this work contributes the following project goals: Develop a building retrofit prioritization strategy for Chicago single-family and 2- to 4-unit buildings; Identify neighborhoods and home types that have the highest potential for savings from electrification; and Assess the impact of advanced building retrofits on energy use, utility bills, and CO2 emissions at the city and building level. Although this study is specific to Chicago, its methods and learnings are applicable across the United States. These findings are especially notable for heat pumps and electrification retrofits in cold climates.

building energy modeling↗
DOE OSTI2023

Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium

Abstract In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Special Nuclear Material Hold-up Measurement

Facilities that process special nuclear material (SNM) generally have a variety of equipment, shielding, and nearby radiation sources, which can pose challenges when performing nondestructive analysis (NDA) within the facility, as shown in Figure 1. In this figure, the left image features two individuals performing a holdup measurement of a large duct at a posting, utilizing a detector probe attached to a yardstick to reduce some aspect of the measurement uncertainty. Note that the distance to the holdup within the pipe from the posting cannot be accounted for. The right image similarly features several individuals guiding a holdup measurement of a ducting pipe several meters overhead, by attaching a detector probe to a long handle and lining that up with a posting on the outside of the pipe. SNM processing begets SNM holdup, and this difficulty with accurate NDA can result in unaccounted accumulation of SNM holdup within a process or area. Normal SNM processing operations can accumulate holdup within filters, pumps, pipes, ducts, other equipment, and facility support systems, as demonstrated by Figure 2. It is important for deactivation and decommissioning (D&D) gloveboxes and their ancillary equipment, material accountability, criticality safety, facility operations, waste management, radiation safety, and security to accurately characterize the location, composition, and quantity of this holdup to minimize these associated risks and potential diversion pathways. Current NDA techniques for assay of holdup are expensive, time consuming, and have high uncertainty.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

The TLK-ASF1 histone chaperone pathway plays a critical role in IL-1β–mediated AML progression

Identifying and targeting microenvironment-driven pathways that are active across acute myeloid leukemia (AML) genetic subtypes should allow the development of more broadly effective therapies. The proinflammatory cytokine interleukin-1β (IL-1β) is abundant in the AML microenvironment and promotes leukemic growth. Through RNA-sequencing analysis, we identify that IL-1β–upregulated ASF1B (antisilencing function-1B), a histone chaperone, in AML progenitors compared with healthy progenitors. ASF1B, along with its paralogous protein ASF1A, recruits H3-H4 histones onto the replication fork during S-phase, a process regulated by Tousled-like kinase 1 and 2 (TLKs). Although ASF1s and TLKs are known to be overexpressed in multiple solid tumors and associated with poor prognosis, their functional roles in hematopoiesis and inflammation-driven leukemia remain unexplored. In this study, we identify that ASF1s and TLKs are overexpressed in multiple genetic subtypes of AML. We demonstrate that depletion of ASF1s significantly reduces leukemic cell growth in both in vitro and in vivo models using human cells. Using a murine model, we show that overexpression of ASF1B accelerates leukemia progression. Moreover, Asf1b or Tlk2 deletion delayed leukemia progression, whereas these proteins are dispensable for normal hematopoiesis. Through proteomics and phosphoproteomics analyses, we uncover that the TLK-ASF1 pathway promotes leukemogenesis by affecting the cell cycle and DNA damage pathways. Collectively, our findings identify the TLK1-ASF1 pathway as a novel mediator of inflammatory signaling and a promising therapeutic target for AML treatment across diverse genetic subtypes. Finally, selective inhibition of this pathway offers potential opportunities to intervene effectively, address intratumoral heterogeneity, and ultimately improve clinical outcomes in AML.

60 APPLIED LIFE SCIENCES↗