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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum

The mechanisms of energy generation and carbon-source utilization in the syphilis spirochete Treponema pallidum have remained enigmatic despite complete genomic sequence information. Whereas the bacterium harbors enzymes for glycolysis, the apparatus for more efficient use of glucose catabolites, namely the citric-acid cycle, is apparently not present. Yet, the organism’s energy needs likely exceed the modest output from glycolysis alone. Recently, building on our structure-function studies of T . pallidum lipoproteins, we proposed a “flavin-centric” metabolic lifestyle for the organism that partially resolves this conundrum. As a part of the hypothesis, we have proposed that T . pallidum contains an acetogenic energy-conservation pathway that catabolizes D-lactate, yielding acetate, reducing equivalents for the generation and maintenance of chemiosmotic potential, and ATP. We already have confirmed the D-lactate dehydrogenase activity in T . pallidum necessary for this pathway to operate. In the current study, we focused on another enzyme ostensibly involved in treponemal acetogenesis, phosphotransacetylase (Pta). This enzyme is putatively identified as TP0094 and, in this study, we determined a high-resolution (1.95 Å) X-ray crystal structure of the protein, finding that its fold comports with other known Pta enzymes. Further studies on its solution behavior and enzyme activity confirmed that it has the properties of a Pta. These results are consistent with the proposed acetogenesis pathway in T . pallidum , and we propose that the protein be referred to henceforth as TpPta.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Broadly neutralizing humanized SARS-CoV-2 antibody binds to a conserved epitope on Spike and provides antiviral protection through inhalation-based delivery in non-human primates

The COVID-19 pandemic represents a global challenge that has impacted and is expected to continue to impact the lives and health of people across the world for the foreseeable future. The rollout of vaccines has provided highly anticipated relief, but effective therapeutics are required to further reduce the risk and severity of infections. Monoclonal antibodies have been shown to be effective as therapeutics for SARS-CoV-2, but as new variants of concern (VoC) continue to emerge, their utility and use have waned due to limited or no efficacy against these variants. Furthermore, cumbersome systemic administration limits easy and broad access to such drugs. As well, concentrations of systemically administered antibodies in the mucosal epithelium, a primary site of initial infection, are dependent on neonatal Fc receptor mediated transport and require high drug concentrations. To reduce the viral load more effectively in the lung, we developed an inhalable formulation of a SARS-CoV-2 neutralizing antibody binding to a conserved epitope on the Spike protein, ensuring pan-neutralizing properties. Administration of this antibody via a vibrating mesh nebulization device retained antibody integrity and resulted in effective distribution of the antibody in the upper and lower respiratory tract of non-human primates (NHP). In comparison with intravenous administration, significantly higher antibody concentrations can be obtained in the lung, resulting in highly effective reduction in viral load post SARS-CoV-2 challenge. This approach may reduce the barriers of access and uptake of antibody therapeutics in real-world clinical settings and provide a more effective blueprint for targeting existing and potentially emerging respiratory tract viruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

FTICR-MS Data from Multi-continent River Water and Sediment and from Coastal River Fresh and Saline Sediment Associated with: “Dissolved Organic Matter Functional Trait Relationships are Conserved Across Rivers”

This data package is associated with the publication “Dissolved Organic Matter Functional Trait Relationships are Conserved Across Rivers” submitted to PNAS (Stegen et al., 2023). The study aims to understand large-scale spatial structure of the dissolved organic matter (DOM) thermodynamic traits and inter-trait relationships by investigating (1) river water and sediments collected along 97 rivers spanning 3 continents and (2) coastal sediment collected from fresh and saline locations in Pacific and Gulf/Atlantic rivers. Sediment extracts and water samples were analyzed using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). This dataset is comprised of three folders (1) Coastal, (2) WHONDR_S19S, and (3) Data_Dictionaries. Coastal contains (1) a subfolder with processed FTICR-MS data as csv files and sample collection metadata, (2) a subfolder with R scripts used to process the data and create associated figures, (3) a subfolder with the raw, unprocessed FTICR-MS data as .xml files, and (4) a readme file with more information about the dataset and instructions for using Formularity (https://omics.pnl.gov/software/formularity). WHONDRS_S19S contains (1) a csv file with processed FTICR data, (2) a csv with sample collection metadata, (3) a csv with sample geospatial data, (4) a csv with simulated lambda model outputs, (5) a subfolder with R scripts used to process the data and create associated figures, and (6) a readme file with more information regarding WHONDRS raw FTICR data and processing scripts. Data_Dictionaries contains data dictionaries for each csv file in the data package. The 97 global river corridors were part of a WHONDRS (https://whondrs.pnnl.gov) study. The raw, unprocessed FTICR-MS data with additional data can be found at doi:10.15485/1729719 for sediments and doi:10.15485/1603775 for water. This data package contains the processed data used in the associated manuscript. The coastal data has not been previously published, and this data package contains both the raw and processed data. Version 3 of this data package published February 2023 includes updates to the title of the manuscript, additional data and data dictionary and updated scripts linked to new analysis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada (CY2020)

This report serves as the combined annual report for post-closure activities in compliance with the requirements listed in Resource Conservation and Recovery Act (RCRA) Permit Number NEV HW0101 associated with the following closed corrective action units (CAUs): 1) CAU 90, Area 2 Bitcutter Containment. 2) CAU 91, Area 3 U-3fi Injection Well. 3) CAU 92, Area 6 Decon Pond Facility. 4)CAU 110, Area 3 WMD U-3ax/bl Crater. 5) CAU 111, Area 5 WMD Retired Mixed Waste Pits. 6) CAU 112, Area 23 Hazardous Waste Trenches. The locations of the sites are shown in Figure ES-1. This report covers calendar year 2020. The post-closure requirements for these sites are described in RCRA Permit NEV HW0101 and are summarized in each CAU-specific section of this report. The results of the inspections, a summary of maintenance activities, and an evaluation of monitoring data are presented in this report.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, NNSS, NV (CY2020, Revision 1)

This report serves as the combined annual report for post-closure activities in compliance with the requirements listed in Resource Conservation and Recovery Act (RCRA) Permit Number NEV HW0101 associated with the following closed corrective action units (CAUs): CAU 90, Area 2 Bitcutter Containment; CAU 91, Area 3 U-3fi Injection Well; CAU 92, Area 6 Decon Pond Facility; CAU 110, Area 3 WMD U-3ax/bl Crater; CAU 111, Area 5 WMD Retired Mixed Waste Pits; CAU 112, Area 23 Hazardous Waste Trenches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada (CY2021)

This report serves as the combined annual report for post-closure activities in compliance with the requirements listed in Resource Conservation and Recovery Act (RCRA) Permit Number NEV HW0101 associated with the following closed corrective action units (CAUs): CAU 90, Area 2 Bitcutter Containment, CAU 91, Area 3 U-3fi Injection Well, CAU 92, Area 6 Decon Pond Facility, CAU 110, Area 3 WMD U-3ax/bl Crater, CAU 111, Area 5 WMD Retired Mixed Waste Pits, and CAU 112, Area 23 Hazardous Waste Trenches. This report covers calendar year 2021. The post-closure requirements for these sites are described in RCRA Permit NEV HW0101 and are summarized in each CAU-specific section of this report. The results of the inspections, a summary of maintenance activities, and an evaluation of monitoring data are presented in this report. This report will address all monitoring requirements noted in the RCRA Permit NEV HW0101, except groundwater monitoring. Groundwater monitoring is documented in the Nevada National Security Site Data Report: Groundwater Monitoring Program Area 5 Radioactive Waste Management Site. All required inspections, maintenance, and monitoring were conducted in accordance with the post-closure requirements of the permit. Revision 6 of RCRA Permit NEV HW0101 was issued effective December 10, 2015, and remained in effect until December 10, 2020. At the time of this report submittal, the new RCRA permit application was in review.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada, For Calendar Year 2021 (Revision 1)

This report serves as the combined annual report for post-closure activities in compliance with the requirements listed in Resource Conservation and Recovery Act (RCRA) Permit Number NEV HW0101 associated with the following closed corrective action units (CAUs): CAU 90, Area 2 Bitcutter Containment; CAU 91, Area 3 U-3fi Injection Well; CAU 92, Area 6 Decon Pond Facility; CAU 110, Area 3 WMD U-3ax/bl Crater; CAU 111, Area 5 WMD Retired Mixed Waste Pits; and CAU 112, Area 23 Hazardous Waste Trenches. This report will address all monitoring requirements noted in the RCRA Permit NEV HW0101, except groundwater monitoring. Groundwater monitoring is documented in the Nevada National Security Site Data Report: Groundwater Monitoring Program Area 5 Radioactive Waste Management Site.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada: For Calendar Year 2020 (Rev. 2)

This report serves as the combined annual report for post-closure activities in compliance with the requirements listed in Resource Conservation and Recovery Act (RCRA) Permit Number NEV HW0101 associated with the following closed corrective action units (CAUs): 1) CAU 90, Area 2 Bitcutter Containment; 2) CAU 91, Area 3 U-3fi Injection Well; 3) CAU 92, Area 6 Decon Pond Facility; 4) CAU 110, Area 3 WMD U-3ax/bl Crater; 5) CAU 111, Area 5 WMD Retired Mixed Waste Pits; 6) CAU 112, Area 23 Hazardous Waste Trenches The locations of the sites are shown in Figure ES-1. This report covers calendar year 2020. The post-closure requirements for these sites are described in RCRA Permit NEV HW0101 and are summarized in each CAU-specific section of this report. The results of the inspections, a summary of maintenance activities, and an evaluation of monitoring data are presented in this report. Site inspections are conducted annually at CAUs 90, 91, and 112; semiannually at CAUs 92 and 110; and quarterly at CAU 111. Additional inspections are conducted at CAUs 92 and 111 if precipitation occurs in excess of 1.0 inch in a 24-hour period. Inspections include an evaluation of the condition of the units, including covers, fences, signs, gates, and locks. At CAUs 110 and 111, soil moisture monitoring and subsidence surveys are conducted in addition to the visual inspections. At CAU 110, the site fence, gate, lock, and use restriction signs are evaluated. At CAU 111, an ecological survey, direct radiation monitoring, air monitoring, radon flux monitoring, and groundwater monitoring are also conducted. This report will address all monitoring item notes above except groundwater monitoring. Groundwater monitoring is documented in the Nevada National Security Site Data Report: Groundwater Monitoring Program Area 5 Radioactive Waste Management Site. All required inspections, maintenance, and monitoring were conducted in accordance with the post-closure requirements of the permit. Revision 6 of RCRA Permit NEV HW0101 was issued effective December 10, 2015, and remained in effect until December 10, 2020. At the time of this report submittal, the new RCRA permit application was in review.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada For Calendar Year 2022

This report serves as the combined annual report for post-closure activities in compliance with the requirements listed in Resource Conservation and Recovery Act (RCRA) Permit Number NEV HW0101 (Rev. 6) associated with the following closed corrective action units (CAUs): CAU 90, Area 2 Bitcutter Containment; CAU 91, Area 3 U-3fi Injection Well; CAU 92, Area 6 Decon Pond Facility; CAU 110, Area 3 WMD U-3ax/bl Crater; CAU 111, Area 5 WMD Retired Mixed Waste Pits; CAU 112, Area 23 Hazardous Waste Trenches. All post-closure inspections and evaluations were performed in accordance with requirements set out in RCRA Permit NEV HW0101, Rev. 6.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Course #2430: Hearing Conservation [Slides]

Occupational hearing loss is one of the most common work-related illnesses in the United States (US). According to OSHA, 22 million US workers are exposed to hazardous noise levels at work, and 25% of these workers will develop permanent hearing loss. Hearing loss from noise is slow and painless, and you can have a disability before you notice it. This course presents the hazards associated with workplace noise, the purpose and elements of the Los Alamos National Laboratory (LANL) Hearing Conservation Program (HCP), and controls that are available to reduce your exposure to hazardous levels of noise.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Energy and economic impacts of U.S. federal energy and water conservation standards adopted from 1987 through 2024

This paper presents estimates of the key impacts of U.S. national energy and water conservation standards adopted from 1987 through 2024. The standards for consumer products, commercial and industrial equipment, lighting products, and plumbing products include those set by legislation as well as standards adopted by the Department of Energy (DOE) through rulemaking. In 2024 alone, these standards are estimated to have saved an estimated 6.0 quads of primary energy, which is equivalent to 6.5% of total U.S. energy consumption, and 1.7 trillion gallons of water, which is equivalent to approximately 12% of the annual water withdrawals for public supply in the U.S in 2015. The estimated reduction in CO 2 emissions associated with the standards in 2024 was 270 million metric tons, which is equivalent to 5.6% of total annual U.S. CO 2 emissions from energy consumption. The annual savings in operating costs for households and businesses totaled $\$$105 billion, and the average household saved $\$$576 in operating costs as a result of standards on residential appliances and plumbing products. The estimated cumulative past and future energy and water savings from these standards amount to 307 quads of energy and almost 53 trillion gallons of water. The estimated cumulative CO 2 emissions reduction from the standards come to 10.3 billion metric tons. Accounting for the increased upfront costs of more-efficient products and the energy and water cost savings over the products’ lifetime, the standards have a cumulative net present value of benefit of $\$$3.2 trillion using 3 percent discount rate and $\$$3.5 trillion using 7 percent discount rate when discounting past and future benefits to 2024.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2026

State Technical Assistance - New Mexico Energy and Conservation Management Division Report [Slides]

The New Mexico Energy and Conservation Management Division (ECMD) sought technical assistance to enhance their ability to evaluate program impacts using the Low-Income Energy Affordability Data (LEAD) tool. NLR assisted ECMD in leveraging the LEAD tool to calculate and analyze energy burden across electric utility service areas, enabling them to assess program outcomes more effectively. To meet ECMD's goals, NLR developed a customized methodology to calculate utility-specific energy burden metrics using census tract data and available utility service area information from the Energy Information Administration (EIA). While acknowledging some limitations in the EIA dataset, NLR estimated the percentage of households within each service territory and incorporated relevant filters such as income, housing characteristics, and other demographics from the LEAD tool. The analysis provided ECMD with a new capability to evaluate program success based on energy savings, reductions in energy burden, and other performance indicators. The data and methodology also support discussions with utilities to improve the accuracy of service territory datasets. ECMD can use the outputs to track program effectiveness and plan future initiatives. NLR offered the possibility of follow-on work, including capacity-building for ECMD to repeat the analysis independently and the option to refine the analysis with updated service.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Scaling Sustainable Biochar Research & Commercialization for Agriculture & Conservation: A Summary from a Stakeholder Convening

Biochar is a carbon-rich substance with the potential to increase soil carbon sequestration, reduce greenhouse gas (GHG) emissions and improve soil health. When used as part of soil health management systems, biochar can provide multiple synergistic benefits for the agricultural sector and society, while also supporting the production of renewable, climate-neutral biofuels. Establishing a pyrolysis biochar bioenergy industry (PBBI) is necessary to harness the environmental benefits of biochar. To galvanize the necessary coordination to support a PBBI, the Foundation for Food & Agriculture Research (FFAR), the National Center for Appropriate Technology (NCAT), and American Farmland Trust (AFT) co-hosted a virtual convening event on biochar research and commercialization in March 2022. Participants represented a diverse set of stakeholders, including biochar producers, agricultural producers, and members of nonprofit, industry and government agencies. This whitepaper offers a summary of the convening, as well as insights from subsequent stakeholder engagement. Sustainably sourced, fit-for-purpose biochar can be a powerful tool in the soil health management systems and climate-smart toolbox, with decades of research supporting the soil, environment, production, and climate benefits. However, because biochar represents a range of feedstocks, processes and products, there is a critical need to: • Coordinate efforts to characterize and test the application of biochar types across locations with diverse soil and management conditions • Address research and decision-support gaps • Support the growing industry These objectives can be addressed or advanced through a coordinated strategy. To support establishment of this strategy, the convening participants identified key gaps in implementation and research. The experiences of foresters, ranchers, and farmers already using biochar, some of whom participated in the convening, helped inform priorities. Key gaps include: • Practical, applied on-farm research • Supporting management for agricultural productivity • Maximum benefits for conservation • Decision support • Life Cycle Assessment (LCA) • Quantification of climate mitigation potential Existing research gaps include: • Potential synergies among biochar, soil organic matter, and enhanced rock weathering • Development of new storage reservoirs for biochar in industrial products Convening participants further provided next steps for rapidly developing a PBBI to produce sustainable, fit-for-purpose biochars that increase soil health and mitigate climate change. Participants also stressed the need for actionable, coordinated, large-scale research relevant to commercial production in the next five years. To have a chance to reduce greenhouse gas emissions, we need an array of tools that would aid in mitigation; a coordinated strategy to enable biochar to be an effective tool in the climate-smart toolbox must be created; We cannot wait 50 years.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Photon (Non)Conservation in the Reduced Speed of Light Approximation and How to (Almost) Fix It

The "Reduced Speed of Light" (RSL) approximation is commonly used to speed up radiative transfer calculations in cosmological simulations. However, it has been shown previously that the RSL approximation leads to photon non-conservation when the radiation field is rapidly evolving in time. I show that these missing photons can be counted exactly for some numerical schemes. Adding them back into a simulation, however, is a much harder task. I show one example of such a scheme, which achieves sub-percent accuracy on simple tests. Unfortunately, the scheme performs much worse on semi-realistic simulations of cosmic reionization, leading to a faster overlap and significant errors in the point-wise comparison of the RSL radiation field with the reference simulation that maintains the full speed of light for the radiative transfer.

Gnedin, Nickolay Y. [Fermilab; Chicago U., KICP; C↗
DOE OSTI2025

Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish

Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studied in vitro and are included in the EPA’s ToxCast program, comprehensive in vivo comparisons using RNA sequencing across structurally diverse agrichemicals, in a single screening platform, are lacking. In this study, we examined structurally diverse agrichemicals found in the U.S. Environmental Protection Agency’s (EPA) Toxcast Phase I and II library by statically exposing early life stage zebrafish at 6 h post fertilization (hpf) until 120 hpf at concentrations ranging from 0.25 to 100 µM. Morphological outcomes were assessed at 120 hpf across 10 endpoints, including yolk sac edema, craniofacial malformations, and axis abnormalities. Chemicals that produced robust concentration-response relationships were selected for transcriptomic profiling. For transcriptomic analysis, zebrafish were statically exposed to each chemical and sampled at 48 hpf, prior to the onset of morphological effects observed at 120 hpf. Differential expression analysis identified between 0 and 4,538 differentially expressed genes (DEGs) per chemical, with no clear correlation to morphological severity. Both DEG and co-expression network analyses revealed chemical-specific expression patterns that converged on shared biological pathways, including neurodevelopment and cytoskeletal organization. Key regulatory genes such as mylpfa and krt4 were identified within co-expression modules, suggesting their potential role in conserved toxicity mechanisms. Semantic similarity analysis of enriched gene ontology (GO) terms, when compared to existing datasets, highlighted gaps in the annotation of neurodevelopmental processes, indicating that some in vivo effects may not be fully captured by current curated resources. The results provide new insights into the modes of action of diverse agrichemicals and establish a framework for understanding how agrichemical structure relates to biological function in a vertebrate model.

agrichemical↗
DOE OSTI2022

Transcriptome Sequencing of Agave angustifolia Reveals Conservation and Diversification in the Expression of Cinnamyl Alcohol Dehydrogenase Genes in Agave Species

Agave angustifolia is an important crassulacean acid metabolism plant species, with wide applications in beverage and sisal fiber production. In this study, we carried out a transcriptome analysis of A. angustifolia leaves, generating a total of 58,482,436 clean reads through Illumina paired-end sequencing. De novo transcriptome assembly generated 67,314 unigenes, with about half of them having homologs in four public databases. In the Nr database, Asparagus officinalis was shown to be most closely related to agave, and the early angiosperm Amborella trichopoda was selected as an outgroup species. We further identified five, two, seven, seven, seven, six and six CAD genes in asparagus, amborella, A. deserti, A. tequilana, A. americana, A. hybrid H11648 and A. angustifolia, respectively. The maximum likelihood phylogenetic tree revealed the species-specific expansion of CAD genes in arabidopsis, rice and agave. The expression analysis indicated the conservatively expressed CAD1/2/4/6, providing candidate targets for manipulation to improve lignin traits. The species-specific expression of CAD3/5/7 indicates the existence of different regulatory mechanisms controlling the expression of these genes in agave species. This study presents the first transcriptome dataset of A. angustifolia, facilitating future studies on lignin biosynthesis in agave.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Rapid Cis–Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4–NOT Component in Drosophila

Young, or newly evolved, genes arise ubiquitously across the tree of life, and they can rapidly acquire novel functions that influence a diverse array of biological processes. Previous work identified a young regulatory duplicate gene in Drosophila, Zeus that unexpectedly diverged rapidly from its parent, Caf40, an extremely conserved component in the CCR4–NOT machinery in post-transcriptional and post-translational regulation of eukaryotic cells, and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome. However, the way in which new DNA-binding proteins acquire and coevolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-Seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we found a dynamic pattern in which Zeus binding rapidly coevolved with a previously unknown DNA motif, which we term Caf40 and Zeus-Associated Motif (CAZAM), under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Using CRISPR-Cas9-mediated gene knockout of Zeus and RNA-Seq, we found that Zeus regulated the expression of 661 differentially expressed genes (DEGs). Our results suggest that the evolution of young regulatory genes can be coupled to substantial rewiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic genome-wide evolutionary processes associated with new genes.

59 BASIC BIOLOGICAL SCIENCES↗