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DOE OSTI2021

Coal-dependent Communities in Transition: Identifying Best Practices to Ensure Equitable Outcomes

The U.S. coal industry is experiencing a sharp increase in the numbers of retired and/or decommissioned coal-fired power plants across the U.S. In the years between 2010-2019, around 102 gigawatts (GW) of coal-fired generating capacity has been announced to be decommissioned, representing more than 546 coal-fired power plant units, and an additional 17 GW is planned to be decommissioned by 2025. This change in the energy production landscape presents an impact on the social, environmental, and economic prospects of coal-dependent communities. This report examined the role of communities in the coal power plant decommissioning process and provided community-identified best practices to ensure an equitable process. The experiences of four coal-dependent communities—Wise County, VA, Muskegon, MI, Anderson County, TN, and Becker, MN—are presented as case studies to understand the impacts of the decommissioning process, and associated best practices, from the communities’ perspective. The report results highlight the need to recognize that the decommissioning decision-making process must be community-based to be equitable. Each community’s input is key to the transition away from coal power because there is no one-size-fits-all development plan. In other words, each community’s trajectory through the decommissioning process—from the retirement decision-making stage to the final site redevelopment phase—is unique because each community has distinct needs and wants from the energy transition. What is best for one community may not be suited for another. Ultimately, the framework for site development and community revitalization post-decommissioning cannot be universal because each community’s profile—from a social, cultural, and economic perspective—is different. Community impacts of power plant decommissioning are not limited to job and revenue losses. Communities are likely to be impacted culturally, socially, environmentally, and have long-term health-based impacts that should be acknowledged and addressed in post-retirement plans. Commonly identified decommissioning best practices include: Early and continued engagement throughout, with a number of mediums for communication and feedback (e.g., in-person sessions, virtual meetings, written comment opportunities); Early planning of post-decommissioning projects to replace lost jobs, revenue, and economic activity; Recognition (and mitigation, if possible) of social impacts on the community due to plant closure; Transparency throughout the process, with trusted information being provided about the decommissioning process and timeline; potential impacts on the workforce, economy, and environment; and the feasibility of alternative site uses; Identification of funding sources, technical experts, and/or strategic partnerships to support decommissioning and the affected communities upfront; and, Acknowledgment of communities as stakeholders who have a role in the conversation and right to determine their futures. Three key areas for assisting coal-dependent communities affected by the energy transition: Technical assistance: assessment of site feasibility for alternative uses or to repower with new technologies; Cross-partnership engagement and collaboration: facilitate knowledge-sharing of “lessons learned” about the decommissioning process between communities and provide guidance for decision-making processes; and, Financial assistance: access to grant and/or loan programs to assist with redevelopment survey, bolster community economic security through job creation, and cover environmental clean-up costs. Technical assistance, cross-partnership engagement, and financial aid can be mobilized to help communities throughout various stages of the decommissioning process, including the retirement decision, the site reclamation phase, and eventual revitalization of the site and surrounding community.

01 COAL, LIGNITE, AND PEAT↗

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↗

DOE OSTI2020

A complete grain-level assessment of the stress-strain evolution and associated deformation response in polycrystalline alloys

Polycrystalline alloys are used pervasively across structural applications contingent upon extensive experimental testing. A statistically representative number of tests are required to expose the variability in the material's performance, as a result of non-uniform microstructures and associated micromechanical fields. In a more direct means of capturing this pertinent information, multi-modal experimental techniques are presented to measure and track the complete micromechanical state, evolving during loading, of each and every grain within the regions of interest. Specifically, a combination of high-energy X-ray diffraction microscopy and digital image correlation coupled with electron backscatter diffraction are conducted on a specimen for each of the alloys, Haynes 282 and Ti7Al. The results of the multi-modal analysis definitively demonstrate that the degree of heterogeneity increases with deformation level and is used to assess the number of grains necessary for a representative volume element description of the stress state for each of these materials. Moreover, higher resolution imaging is used for identification of the slip system activity and subsequently used to study slip transmission events. An accurate knowledge of the resolved shear stress in adjacent grains (grain interactions) is demonstrated to be a key descriptor of the slip transmission events.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Enter Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics

Identifying small molecules (e.g., metabolites) is key towards driving scientific advancement in metabolomics, and gas chromatography–mass spectrometry (GC-MS) is an analytic method that may be applied to facilitate this process. The typical GC-MS identification workflow involves quantifying the similarity of an observed sample spectrum and other features (e.g. retention index) to that of several references, noting the compound of the best-matching reference spectrum as the identified metabolite. While a deluge of similarity metrics exists, none characterize the error rate of generated identifications, thereby presenting an unknown risk of false identification or discovery. To quantify this unknown risk, we propose a model-based framework for estimating the false discovery rate (FDR) among a set of identifications. Extending the traditional mixture modeling framework, our method incorporates both similarity score and experimental information in estimating the FDR. We apply these models to identification lists derived from across 548 samples of varying complexity and sample type (e.g., fungal species, standard mixtures, etc.), comparing their performance to that of the traditional Gaussian mixture model (GMM). Through simulation, we additionally assess the impact of reference library size on the accuracy of FDR estimates. In comparing the best performing model extensions to the GMM, our results indicate relative decreases in median absolute estimation error (MAE) ranging from 12% to 70%, based on comparisons of the median MAEs across all hit-lists. Results indicate that these relative performance improvements generally hold despite library size, however FDR estimation error typically worsens as the set of reference compounds diminishes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

DEVELOPMENT OF AN APPROACH FOR DOWNBLENDING AND DISPOSITION OF IRRADIATED GRAPHITE FUEL

The IGR reactor, a pulse-type test experimental reactor, reached full power in 1961. The reactor contains a center axial experimental ampoule that is subjected to a large pulse of neutrons (neutron flux maximum density of 7×1016 n/cm2·s, peak power 10GW) when the reactor is operated. The fuel form for the IGR reactor is graphite cubes and rods impregnated with highly enriched (90%) uranyl-dinitrate (UO2(NO3)2·6H2O). This fuel is eligible for return to Russia for reprocessing under the Russian Research Reactor Fuel Return program. However due to some technical and licensing issues it was decided to immobilize this fuel in Kazakhstan. The disposition approach thus selected for the spent HEU fuel involves down-blending of the fuel followed by cementation. Development of the process for down-blending and subsequent cementation requires a process that satisfies many criteria, including fissile content, compressive strength, permeability, and containment of radioactivity, among others. One key goal of the final product is to meet the criteria for termination of safeguards. This paper will describe the overall challenge associated with disposition of irradiated HEU graphite spent fuel, the identification of the objectives of the disposition process, and the constraints associated with development of the process and the waste form.

Gaines, Kris↗

DOE OSTI2020

Automated Data Review of Analytical Laboratory Results at Los Alamos National Laboratory - 20299

Newport News Nuclear BWXT-Los Alamos, LLC (N3B) collects samples in support of the U.S. Department of Energy's (DOE) Office of Environmental Management (EM) Los Alamos Legacy Cleanup Contract (LLCC). N3B receives and reviews over 1.6 million sample data points annually in support of various ongoing environmental monitoring and remediation projects of the LLCC. N3B must demonstrate and document that reported external analytical laboratory data produced for the LLCC are of sufficient quality to fulfill their intended purpose and to support defensible decision making as described in EPA QA/G4 Guidance for the Data Quality Objectives Process 1994. In 2018, N3B assumed management of the LLCC along with the Environmental Information Management (EIM) database that contains all historical and current environmental data associated with the LLCC. The entire EIM database is shared between N3B, Triad National Security, LLC (Triad), and New Mexico Environment Department (NMED). These three parties jointly manage the database, its configuration, and changes / updates. All environmental data that are entered into EIM are updated and available, on a daily basis, in the linked public database Intellus New Mexico (Intellus). The quality and defensibility of the environmental data generated from sampling activities is a key component of an effective remediation process. Providing quality data is accomplished through a data assessment process that includes examination, verification, and validation. Examination is the assessment of completeness of the deliverables, identification of any reporting errors, and determining the usability of the data based on the laboratory's evaluation of its data as described in the case narrative received with the data. Verification consists of an evaluation of the Electronic Data Deliverables (EDD) data report to determine the extent to which the external analytical laboratories met method and contract-specific quality control and reporting requirements. Validation consists of determining the data quality and the extent to which the external analytical laboratories accurately and completely reported all sample and quality control results and satisfied all contract requirements. EIM contains an automatic Data Validation Module which performs automated data review (DVM ADR). DVM ADR is a tool to assist in the validation process. When DVM ADR is used in conjunction with manual examination of sample data packages, the combination of the two will meet and exceed the requirements of verification. N3B recognized an opportunity for process improvement, focusing on DVM ADR configuration and enhancements in EIM. Testing EIM's configuration provided proof of the DVM ADR's capabilities and flexibility to accurately perform routine data checks based on analytical methods and regulatory requirements. In addition, the DVM ADR module was improved through enhancements for all analytes, particularly upgrades for radiochemistry data. Extensive testing of the DVM ADR module occurred using EDDs from actual laboratory analyses on the EIM testing site. During this process, N3B manipulated EDD information to verify that the actual outcomes matched the expected outcomes. The results of this testing were shared with the database architects, and configuration improvements were identified to address these results. During this process, N3B identified that the radiochemical DVM ADR capabilities were underutilized, and so enhanced the DVM ADR functionality with respect to radioanalytical assessment. N3B environmental data uploads to Intellus on a daily basis from EIM, once the analytical data undergoes examination and verification. As such, it is important to have a high level of confidence in the quality and defensibility of the data. The process of manual examination, along with the DVM ADR, in conjunction with full validation of a percentage the data specified through the Data Quality Objectives greatly increases efficiency of data review and confidence level of the quality of the data, and gives the project managers, governmental offices, and the public expedited access to high-quality data. (authors)

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DOE OSTI2020

Safety Functions and Features, Events and Processes for the E-Area Performance Assessment

The DOE Technical Standard, “Disposal Authorization Statement and Tank Closure Documentation,” (DOE 2017) recommends the use of safety functions and features, events and processes (FEPs) to support development of conceptual models and identification of scenarios to be considered in a performance assessment (PA). The FEP process provides a means to describe how a PA considers and addresses the factors that could influence the performance of key barriers. Understanding the roles of barriers in terms of limiting migration helps to focus on how changes in the system could lead to a situation where those roles cannot be fulfilled and there is the potential for compromised performance. The FEPs screening and review process was used to identify FEPs that are relevant for the EArea Low-Level Waste Facility (LLWF) and specifically those FEPs that could have a detrimental impact on the effectiveness of a given safety function. For this PA, a default list of FEPs developed at the International Atomic Energy Agency (IAEA 2004) and an approach implemented for PAs at the Hanford and Idaho sites (Mehta et al. 2016, DOE-ID 2019) are used to identify processes and events that could influence the effectiveness of a given safety function for the E-Area LLWF (e.g., subsidence can impact the safety function of the cover system and lead to increased infiltration). The Hanford and Idaho PAs represent two of the most recent applications of this approach. The PA evaluates the potential impacts of changes in performance of different features of the system and demonstrates that the safety functions represent multiple and redundant barriers. Barrier analyses, assuming a safety function is not present, also test the robustness of the system in the event of the loss of one or more safety functions. Such evaluations also support a qualitative illustration of the concept of defense in depth. The safety concept for closure of the E-Area LLWF (generically referred to as “E-Area”) encompasses a variety of different features (i.e., administrative controls, natural site features, and engineered barriers) that reduce the potential impacts on human health and the environment from the residual waste that will remain after closure. These features can be represented as a collection of safety functions acting independently and as a system to provide for overall safety. In some applications, there have been attempts to assign numerical expectations to specific safety functions, but that is not the intent in this case. The concept of safety functions is used more qualitatively in two ways for this PA: 1. To illustrate the robustness of the E-Area design, operational practices and closure approach by documenting features that are and are not credited in different modeling cases. 2. To identify the roles of the different features and potential processes and events that could compromise the performance of safety features and need to be considered when developing the modeling approach. This report addresses both safety functions and FEPs for the E-Area PA.

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DOE OSTI2023

Understanding and Predictability of Integrated Mountain Hydroclimate (Workshop Report)

Mountainous systems cover approximately 23% of Earth’s land and are distributed across all continents. They can capture and store atmospheric moisture that is then cycled through the terrestrial surface and subsurface system, released to downstream communities, and cycled back to the atmosphere. Mountain hydroclimate—characterized by steep gradients, geological, ecological, and biogeochemical diversity—is influenced by topographic forcing and elevated warming and susceptible to large subseasonal to multidecadal variability and rapid changes. Terrestrial hydrological and biogeochemical cycles also experience cascading effects from global warming impacts, such as multidecadal declines in mountain snowpack, longer growing seasons, and increased frequency and severity of extreme events like droughts and wildfires. However, little is known about the effects of these impacts and their feedbacks on climate systems and surface-subsurface compartments. Also unknown are the full implications of changing hydroclimate and extreme events on hydro biogeochemical cycles across atmosphere, terrestrial, and human systems in mountain regions and beyond. This knowledge gap is critical, given human reliance on mountain systems for stable water supply and quality. Mountain systems’ increasing vulnerability to climate change and human perturbations motivates the need to improve understanding of integrated mountain hydroclimate (IMHC) systems and their feedbacks and impacts on humans across scales. However, due to large heterogeneity and strong gradients, coupled natural-human processes in mountain regions present significant challenges for observations, modeling, predictions, and projections. Motivated by gaps in mountain hydroclimate understanding, observations, and modeling and the need for credible projections of future changes, the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program organized a virtual workshop on “Understanding and Predictability of Integrated Mountain Hydroclimate.” Sponsored by BER’s Earth and Environmental Systems Sciences Division (EESSD), the workshop aimed to inform and catalyze EESSD’s growing interests in enhancing predictive understanding of IMHC. Organizers structured the workshop to identify (1) knowledge gaps, (2) observational and modeling challenges, (3) short-term (1 to 3 years) and long-term (10 years and beyond) research opportunities, and (4) strategies for fostering collaboration and coordination. To address the outstanding challenges of IMHC, the workshop included two sessions organized by disciplinary, cross-disciplinary, and crosscutting science topics. The disciplinary and cross-disciplinary topics focused on essential IMHC elements: atmosphere, terrestrial, and human systems and their interactions. Breakout sessions on disciplinary and cross-disciplinary topics facilitated identification of crosscutting topics and central emerging themes. Session 1 focused on connecting existing DOE investments to accelerate progress related to scientific challenges in understanding mountain hydroclimate. In Session 2, participants further explored key Session 1 takeaways through the lens of multiagency collaborations and coordination.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Operational Process for Trigger Identification and Comprehension (OPTIC)

The Operational Process for Trigger Identification and Comprehension (OPTIC) is a standalone, downloadable application designed to enhance the CyOTE (Cybersecurity for the Operational Technology Environment) methodology and will be made available for free download to industry. OPTIC brings key CyOTE functionalities into focus. OPTIC aids OT professionals in analyzing and determining whether an observed anomaly may indicate possible malicious activity or merely a maintenance related irregularity.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

Laser-Induced Fluorescence for Monitoring Environmental Contamination and Stress in the Moss Thuidium plicatile

The ability to detect, measure, and locate the source of contaminants, especially heavy metals and radionuclides, is of ongoing interest. A common tool for contaminant identification and bioremediation is vegetation that can accumulate and indicate recent and historic pollution. However, large-scale sampling can be costly and labor-intensive. Hence, non-invasive in-situ techniques such as laser-induced fluorescence (LIF) are becoming useful and effective ways to observe the health of plants through the excitation of organic molecules, e.g., chlorophyll. The technique presented utilizes images collected of LIF in moss to identify different metals and environmental stressors. Analysis through image processing of LIF response was key to identifying Cu, Zn, Pb, and a mixture of the metals at nmol/cm 2 levels. Specifically, the RGB values from each image were used to create density histograms of each color channel’s relative pixel abundance at each decimal code value. These histograms were then used to compare color shifts linked to the successful identification of contaminated moss samples. Photoperiod and extraneous environmental stressors had minimal impact on the histogram color shift compared to metals and presented with a response that differentiated them from metal contamination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Toward autonomous design and synthesis of novel inorganic materials

Autonomous experimentation driven by artificial intelligence (AI) provides an exciting opportunity to revolutionize inorganic materials discovery and development. Herein, we review recent progress in the design of self-driving laboratories, including robotics to automate materials synthesis and characterization, in conjunction with AI to interpret experimental outcomes and propose new experimental procedures. We focus on efforts to automate inorganic synthesis through solution-based routes, solid-state reactions, and thin film deposition. In each case, connections are made to relevant work in organic chemistry, where automation is more common. Characterization techniques are primarily discussed in the context of phase identification, as this task is critical to understand what products have formed during synthesis. The application of deep learning to analyze multivariate characterization data and perform phase identification is examined. To achieve “closed-loop” materials synthesis and design, we further provide a detailed overview of optimization algorithms that use active learning to rationally guide experimental iterations. Lastly, we highlight several key opportunities and challenges for the future development of self-driving inorganic materials synthesis platforms.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Integrating Advanced Modeling and Accelerated Testing for a Modernized Fuel Qualification Paradigm

With the increasing interest in sodium fast reactor technology, as seen by applications to the U.S. Nuclear Regulatory Commission for the OKLO Aurora plant, fuel testing for the TerraPower Traveling Wave Reactor, and the impending construction and startup of the versatile test reactor (VTR), a modernized, accelerated approach to fuel qualification is needed. To guide this effort, a Phenomena Identification Ranking Table–styled analysis was performed for a U-Pu-Zr sodium-free annular fuel system. This analysis evaluated a series of fuel design properties and parameters against their contributions to key fuel performance phenomena. The resulting priority parameters were then reviewed against existing modeling and experimental capabilities to support investigation of the highest-priority parameters. A pathway for qualification was then established using highthroughput, high-volume experiments from MiniFuel and FAST in parallel with advanced physics-based model development. This effort outlines how the first stages of qualification can be reduced from the typical 20+-year development cycle to 5 to 7 years by deploying accelerated irradiation testing platforms. As with any accelerated test, these methods are prototypic in some aspects and less so in others; however, by coupling with advanced fuel performance modeling and simulation capabilities, the larger space of irradiation parameters and material response provided offers advantages for the validation of physics-based models supporting the deployment of novel fuel designs. As a test case, this paper utilizes a proposed Mark II fuel system for the upcoming VTR. Thus, an accelerated qualification method can be tested for the development of MARK II driver fuel so that by the time of VTR startup, lead test assemblies for a Mark II fuel can be initiated.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase

Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there is a lack of systematic identification and study of TPS in Mentha plants. In this work, we genome-widely identified and analyzed the TPS gene family in Mentha longifolia, a model plant for functional genomic research in the genus Mentha. A total of 63 TPS genes were identified in the M. longifolia genome sequence assembly, which could be divided into six subfamilies. The TPS-b subfamily had the largest number of genes, which might be related to the abundant monoterpenoids in Mentha plants. The TPS-e subfamily had 18 members and showed a significant species-specific expansion compared with other sequenced Lamiaceae plant species. The 63 TPS genes could be mapped to nine scaffolds of the M. longifolia genome sequence assembly and the distribution of these genes is uneven. Tandem duplicates and fragment duplicates contributed greatly to the increase in the number of TPS genes in M. longifolia. The conserved motifs (RR(X)8W, NSE/DTE, RXR, and DDXXD) were analyzed in M. longifolia TPSs, and significant differentiation was found between different subfamilies. Adaptive evolution analysis showed that M. longifolia TPSs were subjected to purifying selection after the species-specific expansion, and some amino acid residues under positive selection were identified. Furthermore, we also cloned and analyzed the catalytic activity of a single terpene synthase, MlongTPS29, which belongs to the TPS-b subfamily. MlongTPS29 could encode a limonene synthase and catalyze the biosynthesis of limonene, an important precursor of essential oils from the genus Mentha. This study provides useful information for the biosynthesis of terpenoids in the genus Mentha.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Analytic techniques for solving the transport equations in electroweak baryogenesis

We develop an efficient method for solving transport equations, particularly in the context of electroweak baryogenesis. It provides fully-analytical results under mild approximations and can also test semi-analytical results, which are applicable in more general cases. Key elements of our method include the reduction of the second-order differential equations to first order, representing the set of coupled equations as a block matrix of the particle densities and their derivatives, identification of zero modes, and block decomposition of the matrix. We apply our method to calculate the baryon asymmetry of the Universe (BAU) in a Standard Model effective field theory framework of complex Yukawa couplings to determine the sensitivity of the resulting BAU to modifications of various model parameters and rates, and to estimate the effect of the commonly-used thin-wall approximation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Chemical structure and genetic organization of the E. coli O6:K15 capsular polysaccharide

Capsular polysaccharides are important virulence factors in pathogenic bacteria. Characterizing the structural components and biosynthetic pathways for these polysaccharides is key to our ability to design vaccines and other preventative therapies that target encapsulated pathogens. Many gramnegative pathogens such as Neisseria meningitidis and Escherichia coli express acidic capsules. The E. coli K15 serotype has been identifed as both an enterotoxigenic and uropathogenic pathogen. Despite its relevance as a disease-causing serotype, the associated capsular polysaccharide remains poorly characterized. We describe in this report the chemical structure of the K15 polysaccharide, based on chemical analysis and nuclear magnetic resonance (NMR) data. The repeating structure of the K15 polysaccharide consists of 4)-α-GlcpNAc-(1→5)-α-KDOp-(2→partially O-acetylated at 3-hydroxyl of GlcNAc. We also report, the organization of the gene cluster responsible for capsule biosynthesis. We identify genes in this cluster that potentially encode an O-acetyltransferase, an N-acetylglucosamine transferase, and a KDO transferase consistent with the structure we report.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

A dynamic protein interactome drives energy conservation and electron flux in Thermococcus kodakarensis

ABSTRACT Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox ( red uction and ox idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated in vivo , particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of bona fide in vivo protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon Thermococcus kodakarensis , were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity in vivo , and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of in vivo assemblies driving ancient metabolic strategies supporting the growth of modern Archaea. IMPORTANCE Given the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by in vivo protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein–protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, Thermococcus kodakarensis , we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity in vivo . These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in T. kodakarensis .

Williams, Sere A. (ORCID:0000000235509590)↗

DOE OSTI2020

Planning for Nuclear Power Plant Site Visits - 20481

The U.5. Department of Energy Office of Integrated Waste Management (DOE-IWM) is planning for future large-scale transport of commercial spent nuclear fuel (SNF) and high-level radioactive waste (HLW) to eventual disposal and/or storage facilities. As part of its planning efforts, DOE conducts evaluations of removing SNF from nuclear power plant sites. Site visits are a pivotal piece in the site evaluations that are conducted by DOE, and significant planning efforts are undertaken to design and implement site visits. Site visits typically include three days of surveys and meetings, including one day each for the nuclear power plant site visit, evaluating near-site transportation infrastructure, and meeting with community engagement panels or advisory boards. This paper outlines DOE-IWM's planning process for conducting nuclear power plant site visits and summarizes the key activities carried out to prepare for a site visit, including a discussion of the background research conducted prior to a site visit. Additionally, the paper describes the development of reference databases for site visits, the identification of unique site characteristics, and the use of geographic information system (GIS) applications to enhance the quality of the information collected during a site visit. (authors)

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