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At least 37 records · Page 2

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

Nitrogen, sulfur and carbon fluxes in the terrestrial subsurface are determined by the intersecting activities of microbial community members, yet the organisms responsible are largely unknown. Metagenomic methods can identify organisms and functions, but genome recovery is often precluded by data complexity. To address this limitation, we developed subsampling assembly methods to re-construct high-quality draft genomes from complex samples. Here, we applied these methods to evaluate the interlinked roles of the most abundant organisms in biogeochemical cycling in the aquifer sediment. Community proteomics confirmed these activities. The eight most abundant organisms belong to novel lineages, and two represent phyla with no previously sequenced genome. Four organisms are predicted to fix carbon via the Calvin Benson Bassham, Wood Ljungdahl or 3-hydroxyproprionate/4-hydroxybutarate pathways. The profiled organisms are involved in the network of denitrification, dissimilatory nitrate reduction to ammonia, ammonia oxidation and sulfate reduction/oxidation, and require substrates supplied by other community members. An ammonium-oxidizing Thaumarchaeote is the most abundant community member, despite low ammonium concentrations in the groundwater. Finally, this organism likely benefits from two other relatively abundant organisms capable of producing ammonium from nitrate, which is abundant in the groundwater. Overall, dominant members of the microbial community are interconnected through exchange of geochemical resources.

60 APPLIED LIFE SCIENCES↗

Genomes to ecosystem function: Targeting critical knowledge gaps in methanogenesis and translation to updated global biogeochemical models (Wrighton Ohio State Report -- Early Career Department of Energy)

In 2018 our key deliverable was a temporally and spatially resolved investigation of the microbial community across wetland soils. As part of this experimental design we sampled 3 land coverage types at a total of 10 sites: Mud (Mud-1, Mud-2, Mud-3), Plant (Nelumbo-1, Nelumbo-2, Nelumbo-3, Typha-1), Open water (Open Water-1, Open Water-2, Open Water-3). Within each site we collected 3-5 soil cores, sub-sampled at the surface (0-5 cm), middle (10- 15 cm), and deep (25-30 cm) depths. Additionally in August, during peak methane emission, we conducted a higher-resolved depth sampling at 5 cm intervals: 0-5, 5-10, 10-15, 15-20, 20-25 and 25-30 cm depths. In total, from a single field season, we collected over 950 samples for paired microbial, geochemical, and metabolite data. Additionally, all measurements were paired to in situ soil greenhouse gas measurements, and emission chamber measurements.

54 ENVIRONMENTAL SCIENCES↗

Genomes to ecosystem function: Targeting critical knowledge gaps in methanogenesis and translation to updated global biogeochemical models

Natural freshwater temperate wetland systems currently represent the largest natural source of atmospheric methane, but are relatively understudied using systems biology tools (e.g. meta-omics) compared to other high producing methane systems (e.g. peat, tropical, or reconstructed wetlands). Using field investigations at the NOAA operated sentinel site on Lake Erie, methane producing activities and responses to geochemical conditions will be determined along seasonal and spatial gradients (Objective 1). Here, a combination of high-throughput activity and gas measurements, combined with high-resolution systems biology and analytical methods, will provide in depth knowledge of the microbiological, chemical, and physical constraints on methane production in wetlands. Using laboratory microcosms, the formation of anoxic microsites and their capacity to facilitate methane production in wetland soils will be simulated (Objective 2). This objective will validate the findings from the field investigations, offering a more controlled environment for teasing out the role of different yet interrelated variables. Lastly, these field and laboratory data will be used for multi-scale, process-level evaluation of an ecosystem biogeochemical model that accommodates these newly identified processes and parameterizes representation of these processes along relevant environmental gradients (Objective 3).This research will identify multiple interacting geochemical, ecological, and metabolic constraints that are poorly understood, oversimplified, or missing in global biogeochemical methane models. This proposal targets the role of oxygen limitation on methane processes in soil domains, to improve reactive transport models of microbial carbon cycling across terrestrial-aquatic soils and generate data on nutrient cycling activities in Great Lake wetlands. This information could provide new insights into the microbial controllers of Lake Erie eutrophication.

59 BASIC BIOLOGICAL SCIENCES↗

Cyber-informed Engineering Microgrid Analysis Tool

The Cyber-Informed Engineering Microgrid Analysis Tool (CIEMAT) leverages the Department of Energy’s Cyber-Informed Engineering to prompt engineering designers and operators through an analysis of the critical functions to be supported by a microgrid installations, the criticality of those functions, the impacts of denial, disruption or misuse of those functions on the microgrid and dependent functions, and the mitigations which could best prevent impacts to those functions resulting from cyber attack. Through use of this tool, microgrid designers and operators can quickly identify appropriate engineering mitigations to limit impacts from cyber attack and functions where engineering and operational staff can prioritize and guide the application of cybersecurity protections to best support the resiliency of the system.

Wright, VirginiaL [Idaho National Laboratory (INL)↗

Cyber-informed Engineering Battery Analysis Tool

The Cyber-Informed Engineering Battery Analysis Tool (CIEBAT) leverages the Department of Energy’s Cyber-Informed Engineering to prompt engineering designers and operators through an analysis of the critical functions to be supported by a BESS installation, the criticality of those functions, the impacts of denial, disruption or misuse of those functions within the BESS system, and the mitigations which could best prevent impacts to those functions resulting from cyber attack. Through use of this tool, BESS designers and operators can quickly identify appropriate engineering mitigation opportunities to limit impacts from cyber attack and functions where engineering and operational staff can prioritize and guide the application of cybersecurity protections to best support the resiliency of the system.

Lampe, BenjaminR [Idaho National Laboratory (INL),↗

An analytic expression approximating the Debye heat capacity function

It is important to have analytic expressions for critical functions in the equations of state of materials. The Debye model has been very successful in approximating the thermal energy properties of a variety of solids, but is nonanalytic. Existing approximations suffer from various shortcomings, the most common being lack of applicability over some temperature range. A new analytic and integrable functional form that closely approximates the Debye model for the heat capacity is presented. This form, based on the mean of two Einstein heat capacity functions with a low temperature correction, exhibits deviations from the Debye model smaller than typical experimental scatter in heat capacity data.

36 MATERIALS SCIENCE↗

Quantifying the sensitivity of ephemeral streams to land disturbance activities in arid ecosystems at the watershed scale

Large areas of public lands administered by the Bureau of Land Management and located in arid regions of the southwestern United States are being considered for the development of utility-scale solar energy facilities. Land-disturbing activities in these desert, alluvium-filled valleys have the potential to adversely affect the hydrologic and ecologic functions of ephemeral streams. Regulation and management of ephemeral streams typically falls under a spectrum of federal, state, and local programs, but scientifically based guidelines for protecting ephemeral streams with respect to land-development activities are largely nonexistent. This study developed an assessment approach for quantifying the sensitivity to land disturbance of ephemeral stream reaches located in proposed solar energy zones (SEZs). The ephemeral stream assessment approach used publicly-available geospatial data on hydrology, topography, surficial geology, and soil characteristics, as well as highresolution aerial imagery. These datasets were used to inform a professional judgment-based score index of potential land disturbance impacts on selected critical functions of ephemeral streams, including flow and sediment conveyance, ecological habitat value, and groundwater recharge. The total sensitivity scores (sum of scores for the critical stream functions of flow and sediment conveyance, ecological habitats, and groundwater recharge) were used to identify highly sensitive stream reaches to inform decisions on developable areas in SEZs. Total sensitivity scores typically reflected the scores of the individual stream functions; some exceptions pertain to groundwater recharge and ecological habitats. The primary limitations of this assessment approach were the lack of high-resolution identification of ephemeral stream channels in the existing National Hydrography Dataset, and the lack of mechanistic processes describing potential impacts on ephemeral stream functions at the watershed scale.The primary strength of this assessment approach is that it allows watershed-scale planning for low-impact development in arid ecosystems; the qualitative scoring of potential impacts can also be adjusted to accommodate new geospatial data, and to allow for expert and stakeholder input into decisions regarding the identification and potential avoidance of highly sensitive stream reaches.

Arid ecosystems↗

Leverage demand-side policies for energy security

Energy security is a top priority for governments, companies, and households because energy systems and the critical functions that they support are threatened by disruptions from wars, pandemics, climate change, and other shocks (1). More often than not, governments rely on policies focused on energy supply to enhance energy security while generally ignoring demand-side possibilities. Further, the indicators traditionally used to measure energy security are also tilted toward the supply side; this fails to capture the full spectrum of vulnerability to energy crises. Energy security assessments need to reflect the wider benefits of security related interventions more accurately. To that end, we develop a systematic approach to measuring the energy security impacts of policy interventions that explicitly considers energy demand (buildings, transport, and industry). Here, we determine that demand-side actions outperform conventional supply-side approaches at making countries more resilient. Energy demand links more directly than supply to the satisfaction of critical social functions and human well-being that are at the core of energy security. Yet, demand-side perspectives tend to be neglected or underrepresented in analysis and policy debates on energy security. Factors that contribute to this supply-side bias include the traditional sectoral organization of industries and policy institutions along fuels (coal, oil, and gas) and energy forms (electric utilities) as well as the decentralized and multivaried activities characteristic of energy demand (from vehicles to household appliances to manufacturing and more), which leads to a multitude of actors and institutional fragmentation. The basic fundamentals of energy systems and markets, where demand and supply are intricately linked, have also not yet risen from vague awareness to a central organizing principle among policy-makers for structuring the energy security discourse.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Data-Model Needs for Belowground Ecology. A Summary Report from the Terrestrial Ecosystem Science (TES) Mini-Workshop, May 8, 2014

Terrestrial life on Earth depends on belowground cycling and storage of a significant portion of the planet’s biologically-active carbon. The interplay among organic inputs by primary producers, soil organic matter stabilization, and assimilation and mineralization by soil organisms drives belowground ecology. Understanding belowground carbon dynamics, including the stability and vulnerability of soil organic carbon stocks, is necessary to project the responses and feedbacks of terrestrial ecosystems to a changing climate. Although conceptually understood, belowground hydrobiogeochemical systems are not well characterized with quantitative and mechanistic representations of critical functions. As a result, these systems are inadequately represented in modeling efforts, limiting our ability to understand and project terrestrial carbon source/sink relationships at various temporal and spatial scales. The belowground science community lacks robust databases and data libraries against which model sensitivities and performance can be tested and enhanced. Improved understanding of belowground ecosystems, including biotic and abiotic interactions, is needed to ensure that model structures include and provide adequate representations of critical belowground processes, functions, and dynamics. A one-day workshop brought together experimental and modeling representatives from the four Department of Energy (DOE) National Laboratories where the Office of Biological and Environmental Research (BER) Terrestrial Ecosystem Science (TES) program has investments in belowground ecology. The group focused on identifying and characterizing (1) critical experimental and observational datasets for testing and developing existing and future belowground-process models and land models; (2) the limitations and needs for modeling belowground processes within ecosystem models; and (3) key areas for leveraging current research activities across the National Laboratories and BER-funded projects. Discussion results are organized in this report as: (I) over-arching data requirements for advancing understanding of belowground ecosystems; (II) efforts that could rapidly improve understanding and model representations of belowground components of terrestrial ecosystems; and (III) longer-term research needs that would benefit from greater and more sustained support.

54 ENVIRONMENTAL SCIENCES↗

Precision Local Positioning System

The primary goal of the project is to lay the groundwork for a new system design, meaning that at the end of this project’s effort, a traditional LLNL project could begin. For this goal to be met, the overarching needs of potential sponsors and stakeholders must be analyzed and understood, and a clear statement of work should be able to be drafted from the finding in this report. More specifically, the results from this project should immediately feed into the drafting of requirements, an implementation plan, and a budget plan for a future project. In order to accomplish this goal, the team set a broad framework for work to be completed. First, conduct current market research and select reference technologies to decompose. From the decompositions, analyze shortcomings, possible pain-points and form metrics and architectural decisions. Next, analyze the potential market area by interviewing/researching stakeholders and understanding their needs. As an additional project goal, attempt to capture as large a market area and scope as reasonably possible by incorporating more than the traditional LLNL sponsors. From the information gathered, study stakeholder salience and understand the relationships between stakeholders, mission areas, mission critical functions, and system metrics. Further analyze the relationships to focus on critical system aspects and to group stakeholders and mission together in order to reduce system complexity while maintaining wide marketability. Finally, begin brainstorming concepts from the established architectural decision and use the found metrics to create tradespaces to down select the most viable architectures. This document presents the team’s findings as it progressed through the project’s strategy.

42 ENGINEERING↗

Automated Vulnerability Detection for Compiled Smart Grid Software

While testing performed with proper experimental controls can provide scientifically quantifiable evidence that software does not contain unintentional vulnerabilities (bugs), it is insufficient to show that intentional vulnerabilities exist, and impractical to certify devices for the expected long lifetimes of use. For both of these needs, rigorous analysis of the software itself is essential. Automated software behavior computation applies rigorous static software analysis methods based on function extraction (FX) to compiled software to detect vulnerabilities, intentional or unintentional, and to verify critical functionality. This analysis is based on the compiled firmware, takes into account machine precision, and does not rely on heuristics or approximations early in the analysis.

99 GENERAL AND MISCELLANEOUS↗

Classical Swine Fever Virus p7 Protein Interacts with Host Protein CAMLG and Regulates Calcium Permeability at the Endoplasmic Reticulum

We have previously shown that Classical Swine Fever Virus (CSFV) p7 is an essential nonstructural protein with a viroporin activity, a critical function in the progression of virus infection. We also identified p7 domains and amino acid residues critical for pore formation. Here, we describe how p7 specifically interacts with host protein CAMLG, an integral ER transmembrane protein involved in intracellular calcium release regulation and signal response generation. Detection of interaction as well as the identification of p7 areas mediating interaction with CAMLG was performed by yeast two-hybrid. p7-CAMLG interaction was further confirmed by confocal microscopy in eukaryotic cells, co-expressing both proteins. Mutant forms of p7 having substituted native residues identified as mediating interaction with CAMLG showed a decreased co-localization compared with the native forms of p7. Furthermore, it is shown that native p7, but not the mutated forms of p7 that fail to interact with CAMLG, efficiently mediates calcium permeability in the ER. Interestingly, viruses harboring some of those mutated forms of p7 have been previously shown to have a significantly decreased virulence in swine.

59 BASIC BIOLOGICAL SCIENCES↗

Functional dichotomy in the 16S rRNA (m 1 A1408) methyltransferase family and control of catalytic activity via a novel tryptophan mediated loop reorganization

Methylation of the bacterial small ribosomal subunit (16S) rRNA on the N1 position of A1408 confers exceptionally high-level resistance to a broad spectrum of aminoglycoside antibiotics. Here, we present a detailed structural and functional analysis of the Catenulisporales acidiphilia 16S rRNA (m 1 A1408) methyltransferase (‘CacKam’). The apo CacKam structure closely resembles other m1A1408 methyltransferases within its conserved SAM-binding fold but the region linking core β strands 6 and 7 (the ‘β6/7 linker’) has a unique, extended structure that partially occludes the putative 16S rRNA binding surface, and sequesters the conserved and functionally critical W203 outside of the CacKam active site. Substitution of conserved residues in the SAM binding pocket reveals a functional dichotomy in the 16S rRNA (m 1 A1408) methyltransferase family, with two apparently distinct molecular mechanisms coupling cosubstrate/ substrate binding to catalytic activity. Our results additionally suggest that CacKam exploits the W203-mediated remodeling of the β6/7 linker as a novel mechanism to control 30S substrate recognition and enzymatic turnover.

59 BASIC BIOLOGICAL SCIENCES↗

Moving from Information Assurance to Functional Assurance with Engineered Controls

Cyber threats to operational technology demand more than traditional IT defenses—they require full-spectrum mission assurance. Cyber-Informed Engineering (CIE) is an approach that embeds engineered controls into system design to ensure critical functions remain safe and reliable, even under attack. Unlike conventional cybersecurity tools, engineered controls act directly on physical processes to prevent unacceptable outcomes such as equipment damage or mission failure. This session will outline the CIE framework and share examples of consequence-based design that deliver true resilience, not just fail-safe behaviors. Attendees will learn how to integrate these principles into the engineering lifecycle to support resilient-by-design architectures and inform emerging standards. This talk sets the stage for the panel discussion on advancing CIE across sectors as digital and physical systems converge.

24 - POWER TRANSMISSION AND DISTRIBUTION↗

Structure, Function and Inhibition of the Phosphoethanolamine Methyltransferases of the Human Malaria Parasites Plasmodium vivax and Plasmodium knowlesi

Phosphoethanolamine methyltransferases (PMTs) catalyze the three-step methylation of phosphoethanolamine to form phosphocholine, a critical step in the synthesis of phosphatidylcholine in a select number of eukaryotes including human malaria parasites, nematodes and plants. Genetic studies in the malaria parasite Plasmodium falciparum have shown that the methyltransferase PfPMT plays a critical function in parasite development and differentiation. The presence of PMT orthologs in other malaria parasites that infect humans and their absence in mammals make them ideal targets for the development of selective antimalarials with broad specificity against different Plasmodium species. Here we describe the X-ray structures and biochemical properties of PMT orthologs from Plasmodium vivax and Plasmodium knowlesi and show that both enzymes are inhibited by amodiaquine and NSC158011, two drugs with potent antimalarial activity. Metabolic studies in a yeast mutant that relies on PkPMT or PvPMT for survival demonstrated that these compounds inhibit phosphatidylcholine biosynthesis from ethanolamine. Our structural and functional data provide insights into the mechanism of catalysis and inhibition of PMT enzymes and set the stage for a better design of more specific and selective antimalarial drugs.

59 BASIC BIOLOGICAL SCIENCES↗

Analysis and improvement of input channel selection algorithm for reliability of control systems in nuclear power plants - 138

In most of non-safety NSSS (Nuclear Steam Supply System) control systems, a process input is composed of two channels for redundancy. In a normal situation, the average of both input channels is used in the control algorithm. If a failed channel is detected, the 'channel selection algorithm' chooses the remaining normal input channel. For a bumpless transition, many implemented control systems include the 'ramping rate' function, which makes it possible for the selected input to slowly approach the new input channel. However, it recently turned out that this function adopted for positive effects may result in unintended consequences for the related control system and the plant in certain cases. Due to a process transient in the plant according to a significant event, any related sensor input signal can rapidly change and finally exceed the pre-defined range for detecting an out-of-range event in a short time. During the process of channel conversion due to a rapid transient in the plant, the processed input from the redundant channels can be distorted if the ramping rate function is not properly implemented. As a result, it can result in a plant shutdown because the control system fails to perform the critical function to mitigate a plant transient. To solve these potential problems, we analyzed the overall causes and derived a proposed algorithm for improving reliability and performance of the control systems. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Municipal and Commercial Equipment for Radiological Response and Recovery in an Urban Environment: State of Science, Research Needs, and Evaluation of Implementation Towards Critical Infrastructure Resilience

This report provides a thorough evaluation of technologies and equipment assets that may be effective at mitigating the effects of a wide-area radioactive contamination event and to restore critical functions to the urban environment. Moreover, equipment that could facilitate decontamination efforts during a recovery phase are evaluated. The summary of methods has been critically evaluated in terms of equipment availability, potential advantages and limitations, and research needs in order to justify and predict its efficacy. By ranking the host of techniques, a concise list of those technologies is provided that might be most impactful to a response and recovery effort and how to direct future effort. The totality of this effort and future work anticipates providing early responders and stakeholders with practical guidance information to expedite an effective response and recovery effort and mitigate the potentially devastating effects of a wide-area radioactive contamination event.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗