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DOE OSTI2025

The Future of a Myriad of Accelerated Biodiscoveries Lies in AI‐Powered Mass Spectrometry and Multiomics Integration

The intersection of modern artificial intelligence (AI) and mass spectrometry (MS) is set to transform the MS‐based “omics” research fields, particularly proteomics, metabolomics, lipidomics, and glycomics, enabling advancements across a wide range of domains, from health to environment and industrial biotechnology. Beginning with an overview of key challenges inherent in MS software pipelines, this personal perspective explores how AI‐driven solutions can address them to enhance data processing, integration and interpretation. It proposes a paradigm shift in molecular identification and quantitation algorithms, leveraging AI to enable holistic interpretation of MS‐based multiomics data. While centered on MS‐based omics, this holistic AI‐driven paradigm is also critical for connecting dynamic biochemical changes to genomics and transcriptomics contexts, reinforcing the integrative value of MS in multiomics research. Ultimately, this AI‐driven approach could enhance efficiency, accuracy, and molecular breadth of coverage, deepening our systems‐level understanding of biological processes and accelerating a myriad of biodiscoveries.

47 OTHER INSTRUMENTATION↗

NASA NTRS2017

Energy in a Planetary Context

The potential present day habitability of solar system bodies beyond Earth is limited to subsurface environments, where the availability of energy in biologically useful form is a paramount consideration. Energy availability is commonly quantified in terms of molar Gibbs energy changes for metabolisms of interest, but this can provide an incomplete and even misleading picture. A second aspect of life's requirement for energy - the rate of delivery, or power - strongly influences habitability, biomass abundance, growth rates, and, ultimately, rates of evolution. We are developing an approach to quantify metabolic power, using a cell-scale reactive transport model in which physical and chemical environmental parameters are varied. Simultaneously, we evaluate cell-specific energy flux requirements and their dependence on environmental "extremes". Comparison of metabolic power supply and demand provides a constraint on how biomass abundance varies across a range of environmental parameters, and thereby a prediction of the relative habitability of different environments. We are evaluating the predictive capability of this approach through comparison to observed distributions of microbial abundance in a range of subsurface (predominantly serpentinizing) systems.

MARINE GEOMICROBIOLOGY↗

DOE OSTI2020

Marine Corps Base Camp Lejeune Climate Forecasts

Critical military training and testing on lands along the nation’s coastal and estuarine shorelines are increasingly placed at risk because of encroachment pressures in surrounding areas, impairments due to other anthropogenic disturbances, and changes in climate and sea level. The U.S. Department of Defense (DoD) intends to enhance and sustain its training and testing assets and also optimize its stewardship of natural resources through the development and application of an ecosystem-based management approach on DoD installations. To accomplish this goal, particularly for installations in estuarine/coastal environments, the Strategic Environmental Research and Development Program (SERDP) launched the Defense Coastal/Estuarine Research Program (DCERP) as a 10-year effort at Marine Corps Base Camp Lejeune (MCBCL) in North Carolina. The results of the second 5 years of the program (DCERP2) are presented in the DCERP2 Final Report.There were four overarching objectives of DCERP2. The first objective was to understand the effects of climate change impacts, including warming temperatures, variability in the hydrological cycle, storm events, and sea level rise on the coastal ecosystems at MCBCL from observations and measurements made over the 10-year program. The second objective was to understand the carbon cycle of the coastal and terrestrial ecosystems at MCBCL through a highly integrated sampling program. The third objective was to develop models, tools, and indicators to evaluate current and projected future ecosystem state changes and translate scientific findings into actionable information for installation managers. The last objective was to recommend adaptive management strategies to sustain ecosystem natural resources within the context of an active military installation.There are 252 mean change files represented in this dataset (12 months * 3 future time periods * 7 variables ). The mean change is calculated by taking the mean of the differences between the future projected average (e.g., 2046-2065) and the climate model baseline (e.g., 1979-1999). The differences were calculated for each downscaled GCM and then averaged across all models to obtain the mean change. This mean of the differences was calculated for each month, each future time period, and each variable.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Evaluating the performance of a high resolution SLIM IM module integrated with an Agilent 6560 IM-QTOF MS - CRADA 413 (Final Report)

Developing new technologies that enhance our abilities to identify molecular signatures is important for the health of the public, the environment, and national security. Deploying these novel technologies requires multiple stages of validation and evaluation. This project focused on evaluating a technology developed at PNNL named Structures for Lossless Ion Manipulations (SLIM) in the context of a commercially available ion mobility mass spectrometer instrument from Agilent Technologies. There is a benefit to integrating the recently developed SLIM module into a real-world instrument platform. Data from the combined instrument will provide new standards for characterizing samples using ion mobility. These standards, related to both the drift time of ions and their resulting collisional cross sections (CCS) will be of value in characterizing samples from both humans and environmental samples, such as soil microbiomes. Because no previous instrument has been designed and implemented to simultaneously analyze the same sample in both constant and oscillating drift fields, the project will provide a new research capability that will support research in a wide variety of applications. The evaluation approach included measuring the resolving power, mass range, sensitivity, and accuracy of two SLIM variations (constant and oscillating fields). Although SLIM performed similarly to the commercial instrument in terms of sensitivity, mass range, and accuracy the resolving power of SLIM far exceeded that of the commercially-available instrument. This validation will provide critically useful data to our commercial partners which they can use to reach informed decisions on the advantages of the SLIM technology such as the outstanding performance and the low cost of manufacturing.

42 ENGINEERING↗

DOE OSTI2022

An Overview of Biofilm Formation–Combating Strategies and Mechanisms of Action of Antibiofilm Agents

Biofilm formation on surfaces via microbial colonization causes infections and has become a major health issue globally. The biofilm lifestyle provides resistance to environmental stresses and antimicrobial therapies. Biofilms can cause several chronic conditions, and effective treatment has become a challenge due to increased antimicrobial resistance. Antibiotics available for treating biofilm-associated infections are generally not very effective and require high doses that may cause toxicity in the host. Therefore, it is essential to study and develop efficient anti-biofilm strategies that can significantly reduce the rate of biofilm-associated healthcare problems. In this context, some effective combating strategies with potential anti-biofilm agents, including plant extracts, peptides, enzymes, lantibiotics, chelating agents, biosurfactants, polysaccharides, organic, inorganic, and metal nanoparticles, etc., have been reviewed to overcome biofilm-associated healthcare problems. From their extensive literature survey, it can be concluded that these molecules with considerable structural alterations might be applied to the treatment of biofilm-associated infections, by evaluating their significant delivery to the target site of the host. To design effective anti-biofilm molecules, it must be assured that the minimum inhibitory concentrations of these anti-biofilm compounds can eradicate biofilm-associated infections without causing toxic effects at a significant rate.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1977

Effects of space radiation on thin polymers and nonmetallics

Advanced materials for various spacecraft systems in the 1980s and 1990s have been evaluated in situ after exposure to space radiation. Emphasis has been placed on materials having little or no previous base of environmental effects data. Applications ranging from earth orbit to near-sun have been covered. High temperature polymers and composites have been included. Silica composites may offer improved reflectance stability compared with metallized fluorocarbons. Directional reflectance properties of FEP are a function of charged particle energy and flux as well as total exposure fluence and material characteristics. Data obtained on polyimides and polyxylylenes under high temperature radiation exposure conditions will be discussed in the context of near-sun solar sailing and rendezvousing.

Fogdall, L. B.↗

NASA NTRS1988

Cretaceous-Tertiary findings, paradigms and problems

The asteroid hypothesis has stimulated numerous studies of the paleontological record at Cretaceous/Tertiary time as well as of geological indicators of environmental crisis preserved in the rock record. Both extinctions and geological anomalies often occur at times that do not appear to be synchronous or instantaneous. The record includes paleontological indicators of dinosaurs, terrestrial flora, marine planktonic organisms, and shallow water marine macrofauna and geological phenomena include occurrences of iridium and other platinum metals, trace elements, clay mineralogy, shocked minerals, soot, microspherules, and isotopes of osmium, strontium and carbon. These findings are reviewed in the context of the alternate hypotheses of an exogenic cause, involving either a single asteroid impact or multiple commentary impacts, and an endogenic cause, involving intense global volcanism and major sea level regression.

Officer, C. B.↗

DOE OSTI2022

CLARIFYING THE NEXUS BETWEEN LIFE CYCLE ASSESSMENT AND CIRCULARITY INDICATORS: A SETAC/ACLCA INTEREST GROUP

Purpose Improving the circularity of resources is important to the sustainability of consumer goods. Current research has indicated that circularity practices and circular economy (CE) methods do not always reduce environmental impacts. The aim of this research is to investigate the adoption of the life cycle assessment (LCA) methodology to improve the environmental impacts of circularity practices. Methods As part of the Society for Environmental Toxicology And Chemistry (SETAC) forum, an interest group (IG) on Circularity and LCA was formed in partnership with the American Center for Life Cycle Assessment (ACLCA) to tackle methodological and technical issues related to circularity in LCA. The IG’s research approach is summarized in four key steps: defining goals and objectives, literature review and gap analysis, ideation, and experimentation. The twelve active persons within this IG meet monthly and have been divided into four sub-working groups (sub-WGs) so that complementary tasks can be completed concurrently in an effective manner. Each sub-WG meets monthly and reports back to the main group for collaboration and brainstorming to meet the research objectives. Results and discussion First, the sub-WG #1, focusing on the “pool of circularity and LCA-based indicators”, analyzed the complementarity between two of the most used circularity indicators and LCA. Second, the sub-WG #2, working on the “evaluation of CE loops performance through LCA”, built a mind map of pain points that reflect the challenges that the LCA practitioners face when combining LCA with CE approaches. Third, the sub-WG #3, dealing with the “trade-offs between circularity and sustainability”, highlighted key alignments and/or conflicts between circularity and sustainability performance depending on the scope, product, industry, or system of analysis. Fourth, the sub-WG #4, focusing on “business and industrial cases”, plans to leverage the knowledge base developed within this IG to develop use cases documenting the benefits and challenges associated with CE-related loops modeling in LCA. Conclusions The first findings of this SETAC/ACLCA IG provide a state-of-the-art overview of the synergists of LCA methodology and the CE measurement frameworks reported in the literature. To move forward and capitalize on the first findings, one valuable point will be to discuss and provide concrete solutions to the pain points that emerged when considering circularity in LCA. Eventually, the knowledge base and resources created within this IG ultimately aim to support the proper application of LCA for practitioners in CE contexts, and could provide relevant inputs for the ISO Technical Committee ISO/TC 323 working on the upcoming standard for the measurement of CE performance.

Life cycle assessment, circular economy, circulari↗

DOE OSTI2021

Importance of suberin biopolymer in plant function, contributions to soil organic carbon and in the production of bio-derived energy and materials

Abstract Suberin is a hydrophobic biopolymer of significance in the production of biomass-derived materials and in biogeochemical cycling in terrestrial ecosystems. Here, we describe suberin structure and biosynthesis, and its importance in biological (i.e., plant bark and roots), ecological (soil organic carbon) and economic (biomass conversion to bioproducts) contexts. Furthermore, we highlight the genomics and analytical approaches currently available and explore opportunities for future technologies to study suberin in quantitative and/or high-throughput platforms in bioenergy crops. A greater understanding of suberin structure and production in lignocellulosic biomass can be leveraged to improve representation in life cycle analysis and techno-economic analysis models and enable performance improvements in plant biosystems as well as informed crop system management to achieve economic and environmental co-benefits.

09 BIOMASS FUELS↗

NASA NTRS2008

NASA's Modern Era Retrospective-Analysis for Research and Applications (MERRA): Early Results and Future Directions

This talk will review the status and progress of the NASA/Global Modeling and Assimilation Office (GMAO) atmospheric global reanalysis project called the Modern Era Retrospective-Analysis for Research and Applications (MERRA). An overview of NASA's emerging capabilities for assimilating a variety of other Earth Science observations of the land, ocean, and atmospheric constituents will also be presented. MERRA supports NASA Earth science by synthesizing the current suite of research satellite observations in a climate data context (covering the period 1979-present), and by providing the science and applications communities with of a broad range of weather and climate data with an emphasis on improved estimates of the hydrological cycle. MERRA is based on a major new version of the Goddard Earth Observing System Data Assimilation System (GEOS-5), that includes the Earth System Modeling Framework (ESMF)-based GEOS-5 atmospheric general circulation model and the new NOAA National Centers for Environmental Prediction (NCEP) unified grid-point statistical interpolation (GST) analysis scheme developed as a collaborative effort between NCEP and the GMAO. In addition to MERRA, the GMAO is developing new capabilities in aerosol and constituent assimilation, ocean, ocean biology, and land surface assimilation. This includes the development of an assimilation capability for tropospheric air quality monitoring and prediction, the development of a carbon-cycle modeling and assimilation system, and an ocean data assimilation system for use in coupled short-term climate forecasting.

Schubert, Siegfried↗

DOE OSTI2024

Climate Impact of Primary Plastic Production

Plastics show the strongest production growth of all bulk materials over the last decade. The industry’s current growth trajectory is exponential and plastic production is expected to double or triple by 2050. The rapidly increasing production of plastics and the continued reliance on fossil fuels for production, have contributed to numerous environmental problems and health harms. As a result, plastic pollution has become an increasing threat to natural ecosystems, human health and climate. However, there is a lack of granularity on the contribution of the primary plastics specifically to greenhouse gas (GHG) emissions and their impact on the remaining global carbon budget needed to stay below a 1.5°C or 2°C global average temperature rise. In this report, we explore the contribution of primary plastic production to climate change disaggregated by polymer and technology. To this end, we have developed comprehensive bottom-up modeling of GHG emissions from global primary plastic production, with a special focus on polymer value chains. We have analyzed the results under various growth scenarios in the context of carbon budgets compatible with a 1.5°C global trajectory. Modeling includes the material flows of all production stages, processes and technologies used in primary plastic production value chains, including from the extraction of fossil fuels required for production to shaping the final product. We specifically focus on nine major types of fossil fuelbased plastic polymers that are produced and consumed in large quantities: three types of polyethylene (PE) – low-density (LDPE), linear low-density (LLDPE), and high-density (HDPE) – as well as polypropylene (PP); polyethylene terephthalate (PET); polyvinyl chloride (PVC); polystyrene (PS) and other key styrene-based plastics such as styrene acrylonitrile (SAN) and acrylonitrile butadiene styrene (ABS), and polyurethane (PU). Together these account for about 80% of plastics production.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2011

Current Status of the Nitrogen Oxygen Recharge System

This paper presents an overview of the Nitrogen Oxygen Recharge System (NORS) to date and the current development status of the system. NORS is an element of the International Space Station (ISS) Environmental Control and Life Support Systems (ECLSS) used to resupply the ISS with Nitrogen and Oxygen following the impending retirement of the Space Shuttle. The paper will discuss why NASA is developing NORS, including a summary of other concepts considered, and other related concepts currently being developed by NASA. The current system architecture will be described, along with a summary of the current design of the NORS. The overall programmatic schedule of the NORS in the context of the upcoming shuttle retirement and future launch vehicle development will also be presented. Finally, the paper will examine the significant technical challenges encountered during the requirements and preliminary design phase of NORS development. A key challenge to the development of NORS is the international shipment - and associated regulations - of pressurized Oxygen, which is necessary due to the use of launch vehicles based in Japan and French Guiana to send NORS gasses to the ISS. The storage and use of relatively large quantities of high pressure (41,000 kPa) Oxygen and Nitrogen within the ISS, which is unprecedented both on the ISS and other space vehicles, has had a significant impact on the design and architecture of the system. The high pressure of the system also poses unique thermal considerations, which has led to the development of a heater system for thermal conditioning of high pressure gas to avoid thermal impacts on downstream hardware. The on-orbit envelope allocated to the NORS has changed (gotten smaller) and has impacted both the design and architecture of the system. Finally, the balance of safety considerations associated with these high pressure gasses, particularly high pressure Oxygen, with the functionality of the system has profoundly impacted the form of the system and will be discussed.

Dick, Brandon↗

DOE OSTI2024

Climate Impact of Primary Plastic Production

Plastics show the strongest production growth of all bulk materials over the last decade. The industry’s current growth trajectory is exponential and plastic production is expected to double or triple by 2050. The rapidly increasing production of plastics and the continued reliance on fossil fuels for production, have contributed to numerous environmental problems and health harms. As a result, plastic pollution has become an increasing threat to natural ecosystems, human health and climate. However, there is a lack of granularity on the contribution of the primary plastics specifically to greenhouse gas (GHG) emissions and their impact on the remaining global carbon budget needed to stay below a 1.5°C or 2°C global average temperature rise. In this report, we explore the contribution of primary plastic production to climate change disaggregated by polymer and technology. To this end, we have developed comprehensive bottom-up modeling of GHG emissions from global primary plastic production, with a special focus on polymer value chains. We have analyzed the results under various growth scenarios in the context of carbon budgets compatible with a 1.5°C global trajectory. Modeling includes the material flows of all production stages, processes and technologies used in primary plastic production value chains, including from the extraction of fossil fuels required for production to shaping the final product. We specifically focus on nine major types of fossil fuel-based plastic polymers that are produced and consumed in large quantities: three types of polyethylene (PE) – low-density (LDPE), linear low-density (LLDPE), and high-density (HDPE) – as well as polypropylene (PP); polyethylene terephthalate (PET); polyvinyl chloride (PVC); polystyrene (PS) and other key styrene-based plastics such as styrene acrylonitrile (SAN) and acrylonitrile butadiene styrene (ABS), and polyurethane (PU). Together these account for about 80% of plastics production.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

$\mathrm{COBRA}$ improves the completeness and contiguity of viral genomes assembled from metagenomes

Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Summary of October 2023 ARM User Executive Committee Meeting

The User Executive Committee (UEC) provides objective, timely feedback to the leadership of the Atmospheric Radiation Measurement (ARM) user facility with respect to the user experience. The UEC held a hybrid meeting at the ARM Southern Great Plains Observatory in October 2023. Four goals were identified for this meeting: (1) to take an in-depth look at the ARM user facility, (2) to provide actionable items to ARM within the context of the UEC subgroups, (3) to develop new user engagement strategies, and (4) to see an ARM facility in operation, providing valuable context for future UEC discussions. The outcomes of the successful meeting are highlighted in this report. The UEC is grateful to ARM for facilitating this in-person meeting and to our gracious hosts at SGP.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Aligning theoretical and empirical representations of soil carbon-to-nitrogen stoichiometry with process-based terrestrial biogeochemistry models

Soil carbon-nitrogen (C:N) stoichiometry acts as a control over decomposition and soil organic matter formation and loss, making it a key soil property for understanding ecosystem dynamics and projected ecosystems responses to global environmental change. However, the controls of soil C:N and how they respond to increasing pressures from global change agents are not fully understood. The “foundational” controls on soil C:N, namely plant and microbial C:N, have been used to predict soil C:N, but fail to accurately simulate all ecosystems and may be insufficient for predictions under global environmental change. Here we present an “emerging” representation of controls of soil C:N that includes plant-microbe-mineral feedbacks that have been shown to regulate soil C:N. We argue that including representation of these emerging drivers in process-based terrestrial biogeochemistry models, which include biological N fixation, mycorrhizae, priming, root exudation of organic acids, and mineralogy (including soil texture, mineral composition, and aggregation), will improve mechanistic representation of soil C:N and associated processes. Such improvements will produce models that will better simulate a variety of ecological states and predict soil C:N when global changes modify plant-microbe-mineral interactions. Here, we align our empirical understanding of controls of soil C:N with those controls represented in models, identifying contexts where emerging drivers might be particularly important to represent (e.g., priming and root exudation in nutrient-limited conditions) and areas of future work. Additionally, we show that implementing emerging drivers of soil C:N results in different simulated outcomes at steady state and in response to elevated atmospheric CO2. Our review and preliminary simulations support the need to incorporate emerging drivers of soil C:N into process-based terrestrial biogeochemistry models, allowing for both theoretical exploration of mechanisms and potentially more accurate predictions of land biogeochemical responses to global change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli

ABSTRACT The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made toward identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N = N-R’), found in diverse chemicals in both food and drugs. Surprisingly, the canonical azoR gene in Escherichia coli was dispensable for azo bond reduction. Instead, azoreductase activity was controlled by the fumarate and nitrate reduction ( fnr ) regulator, consistent with a requirement for the anoxic conditions found within the gastrointestinal tract. Paired transcriptomic and proteomic analysis of the fnr regulon revealed that in addition to altering the expression of multiple reductases, FNR is necessary for the metabolism of L-Cysteine to hydrogen sulfide, enabling the degradation of azo bonds. Furthermore, we found that FNR indirectly regulates this process through the small noncoding regulatory RNA fnrS . Taken together, these results show how gut bacteria sense and respond to their intestinal environment to enable the metabolism of chemical groups found in both dietary and pharmaceutical compounds. IMPORTANCE This work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and nonenzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen, and L-Cysteine control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

CCUS Perspectives: Assessing Historical Contexts, Current Realities, and Future Prospects

CCUS technologies are crucial solutions for mitigating climate change by reducing CO2 emissions from industrial operations and energy sectors. This review critically examines the current state of CCUS technologies, and highlights advancements, challenges, regulatory frameworks, and future directions. It comprehensively analyzes carbon capture methods, such as pre-combustion, post-combustion, and oxy-fuel combustion capture, while comparing their efficiencies and limitations. The review also explores carbon utilization techniques, such as direct and indirect utilization, emphasizing their potential applications and technological constraints. Additionally, it assesses various carbon storage methods, focusing on geological, ocean, and mineralization storage, and discusses their capacity, feasibility, and environmental implications. The study reviews the policy and regulatory frameworks, economic viability, market trends, and environmental sustainability of CCUS. By identifying research gaps and recommending future research priorities, this review aims to guide the development of more efficient/effective, and cost-effective CCUS technology, ensuring their role in a sustaining low-carbon future. This review provides a forward-looking perspective, a critical and interdisciplinary analysis that assesses the current state of CCUS technologies, and further provides a roadmap for future development.

Energy & Fuels↗