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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Group VII ethylene response factors forming distinct regulatory loops mediate submergence responses

Group VII ethylene response factors (ERFVIIs), whose stability is oxygen concentration-dependent, play key roles in regulating hypoxia response genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) during submergence. To understand the evolution of flooding tolerance in cereal crops, we evaluated whether Brachypodium distachyon ERFVII genes (BdERFVIIs) are related to submergence tolerance. We found that three BdERFVIIs, BdERF108, BdERF018, and BdERF961, form a feedback regulatory loop to mediate downstream responses. BdERF108 and BdERF018 activated the expression of BdERF961 and PHYTOGLOBIN 1 (PGB1), which promoted nitric oxide turnover and preserved ERFVII protein stability. The activation of PGB1 was subsequently counteracted by increased BdERF961 accumulation through negative feedback regulation. Interestingly, we found that OsERF67, the orthologue of BdERF961 in rice, activated PHYTOGLOBIN (OsHB2) expression and formed distinct regulatory loops during submergence. Overall, the divergent regulatory mechanisms exhibited by orthologs collectively offer perspectives for the development of submergence-tolerant crops.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase

The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families inArabidopsis) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein–protein and co-occurrence interactions, informed by gene network patterns using the STRING database, inArabidopsis thalianaandChlamydomonas reinhardtiiunveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified inArabidopsis, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory. This article is part of the theme issue ‘The evolution of plant metabolism’.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Engineering quantitative stomatal trait variation and local adaptation potential by cis‐regulatory editing

Summary Cis‐regulatory element editing can generate quantitative trait variation that mitigates extreme phenotypes and harmful pleiotropy associated with coding sequence mutations. Here, we applied a multiplexed CRISPR/Cas9 approach, informed by bioinformatic datasets, to generate genotypic variation in the promoter ofOsSTOMAGEN, a positive regulator of rice stomatal density. Engineered genotypic variation corresponded to broad and continuous variation in stomatal density, ranging from 70% to 120% of wild‐type stomatal density. This panel of stomatal variants was leveraged in physiological assays to establish discrete relationships between stomatal morphological variation and stomatal conductance, carbon assimilation and intrinsic water use efficiency in steady‐state and fluctuating light conditions. Additionally, promoter alleles were subjected to vegetative drought regimes to assay the effects of the edited alleles on developmental response to drought. Notably, the capacity for drought‐responsive stomatal density reprogramming instomagenand two cis‐regulatory edited alleles was reduced. Collectively our data demonstrate that cis‐regulatory element editing can generate near‐isogenic trait variation that can be leveraged for establishing relationships between anatomy and physiology, providing a basis for optimizing traits across diverse environments.

Biotechnology & Applied Microbiology↗
DOE OSTI2026

Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA-seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co-expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co-expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA-seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day-length, shading, water-deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

RNA-seq↗
DOE OSTI2026

Cis-regulatory evolution shapes facial diversity in birds and mammals

Birds and mammals exhibit extraordinary facial diversity, reflecting adaptations to distinct ecological niches and feeding strategies. While core face-building developmental programs are conserved and orchestrated by interactions between ectodermal organizers and the underlying mesenchyme, mechanisms driving facial shape variation remain poorly understood. Here, we integrate single-cell transcriptomic and chromatin accessibility profiling of mouse and chicken developing face to construct a comparative regulatory map. Although both ectodermal and mesenchymal populations display distinct regulatory features in each species, the mesenchyme exhibits markedly greater divergence, pointing to its central role in shaping facial morphology. We further reveal unexpected molecular complexity in the main face-shaping organizer, including a mouse-specific Shh/Wnt5a expression domain. At key morphogen loci (Bmp4, Fgf8, and Wnt5a), conserved and lineage-specific enhancers exhibit spatially restricted activity patterns that mirror divergent signaling domains. These findings demonstrate how cis-regulatory evolution modulates conserved developmental programs to generate morphological novelty, providing a valuable resource for studying vertebrate facial evolution.

Kyomen, Stella [Max Planck Institute for Evolution↗
DOE OSTI2024

Established Regulatory Limits for Surface Water and Groundwater

The regulatory limits for surface water and groundwater contained in this database comprise chemical-specific preliminary remediation goals (PRGs) based on potential Applicable or Relevant and Appropriate Requirements (ARARs). These values should be used in conjunction with PRGs based on risk assessment to ensure that the PRGs for a site meet the residual risk requirements for protection of human health and the environment in the National Oil and Hazardous Substance Pollution Contingency Plan (NCP). In some cases, the values presented in this database may be To-Be-Considered (TBC) Guidance because these values are superseded by site-specific state requirements. ARARs are available for the Federal government, California, Georgia, Illinois, Kentucky, New Jersey, New Mexico, Nevada, New York, Ohio, South Carolina, Tennessee, Washington, and Wisconsin. The dataset provides maximum contaminant levels for drinking water and water quality criteria for fresh and marine environments based on acute and chronic exposures. Users can select ARAR sources, drinking water standards and water quality standards, individual chemicals, and retrieve results in tabular or spreadsheet formats for analysis. ARARs are derived from authoritative sources, including federal and state government agencies. The dataset supports environmental risk assessments, regulatory decision-making, and environmental planning, with tools for benchmarking against promulgated standards. This structured approach ensures a robust evaluation of environmental risks tailored to regulatory needs.

Stewart, Debra [Oak Ridge National Laboratory (ORN↗
DOE OSTI2024

A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution

Abstract Only a handful of somatic alterations have been linked to endocrine therapy resistance in hormone-dependent breast cancer, potentially explaining ∼40% of relapses. If other mechanisms underlie the evolution of hormone-dependent breast cancer under adjuvant therapy is currently unknown. In this work, we employ functional genomics to dissect the contribution of cis-regulatory elements (CRE) to cancer evolution by focusing on 12 megabases of noncoding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. Parallel epigenetic perturbation (CRISPRi) in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance and endocrine therapy resistance. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies a limited set of noncoding changes potentially involved in therapy resistance. Overall, our data uncover how endocrine therapies trigger the emergence of transient features which could ultimately be exploited to hinder the adaptive process. Significance: This study shows that cells adapting to endocrine therapies undergo changes in the usage or regulatory regions. Dormant cells are less vulnerable to regulatory perturbation but gain transient dependencies which can be exploited to decrease the formation of dormant persisters.

Oncology↗
DOE OSTI2023

Functional characterization and regulatory modeling of lignocellulose deconstruction in the saprophytic bacterium Cellvibrio japonicus (Final Technical Report)

The goal of this project was to establish a fundamental systems-level model of lignocellulose deconstruction by saprophytic soil bacteria while simultaneously identifying and characterizing novel enzymes that can be used for applied bioenergy technologies. This project was significant because it elevated our mechanistic and regulatory understanding of bacterial plant biomass degradation and led to technologies to enable bottlenecks in biofuel production R&D. Furthermore, the completed work was novel because it integrated in vivo, in vitro, and in silico approaches with bioenergy-relevant substrates. We identified the required enzymes for lignocellulose degradation and mechanisms of regulation through a combination of transcriptomic profiling (RNAseq), enzymatic analysis, the functional characterization of mutants, and modeling of the regulatory networks used to detect and degrade lignocellulose. This project employed the lignocellulose-degrading bacterium Cellvibrio japonicus to dissect the functional properties and underlying regulatory networks saprophytic bacteria use to depolymerize and utilize lignocellulose. There were four Objectives to this project, the specific metrics of which are summarized in this report.

09 BIOMASS FUELS↗
DOE OSTI2023

Addressing Regulatory Challenges to Tribal Solar Deployment

This project, Addressing Regulatory Challenges to Tribal Solar Deployment, seeks to unlock some of this potential by bringing Tribal, regulatory, utility, and other stakeholders together to articulate key barriers to Tribal solar adoption and develop replicable solutions. By increasing institutional capacity and developing frameworks, trainings, and a technical document repository for regulatory bodies, utilities, and Tribes, this project can help expand an emerging market.

14 SOLAR ENERGY↗
DOE OSTI2023

USAID Colombia Young Leaders Workforce Training Program Action Plans: Regulatory Road Map for Distributed Energy Resource (DER) Interconnection and Interoperability

As part of the U.S. Agency for International Development (USAID)-National Renewable Energy Laboratory (NREL) Young Leaders Workforce Training Program in Colombia, participants from Colombia's Energy and Gas Regulatory Commission (CREG) leveraged their training and professional experience to develop a regulatory roadmap for the interconnection and interoperability of increasing integration of distributed energy resources (DERs). CREG was one of four teams selected by the training program development team to receive continued technical assistance and strategic advisory support from the USAID-NREL Partnership for action plan development and implementation. This case study provides an overview of the key activities and outcomes of the technical assistance provided by NREL on the CREG Action Plan, and key next steps for implementation of Colombia's DER Integration Regulatory Roadmap.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Definition and Execution of Regulatory requirements for acceptance of the Whooshh Fish Transport System (Abstract)

The purpose of this project is to assist in the definition, summarization, and execution of the regulatory requirements that validate the Whooshh Fish Transport System (WFTS) as an accepted method of fish passage transport for Endangered Species Act- (ESA) listed species; moving these fish past in-stream barriers, such as hydropower facilities. Validation of this technology, through testing by PNNL, means that regulatory agencies will have documented evidence from which to support an approval decision enabling Whooshh to quickly commercialize their product for use in waterways with ESA listed species and provide the hydropower relicense/development marketplace a viable solution to the fish passage problem that threatens the hydropower industry. Given the definition of “take” in the ESA, without validation, commercialization in this space in the U.S. will not happen because the regulatory agencies will not have the determinative study results they require to authorize the use of this new technology that interact with ESA-listed species.

13 HYDRO ENERGY↗
DOE OSTI2026

Reassessing Double-Ended Guillotine Break Requirements: Evidence-Based Analysis of Regulatory Assumptions After Five Decades of Nuclear Operation

After five decades of nuclear power operation encompassing more than 20,000 reactor-years across 35 countries and 647 reactors, zero double-ended guillotine breaks (DEGBs) have been documented in commercial reactor coolant systems—despite DEGB being the fundamental design-basis assumption driving Emergency Core Cooling System (ECCS) sizing, structural protection requirements, and containment design specifications. This report examines the basis for DEGB requirements in nuclear power plant design. The DEGB postulate assumes the instantaneous, complete circumferential severance of the largest diameter pipes in reactor coolant systems, driving major design requirements under 10 Code of Federal Regulations 50.46, General Design Criterion 4 and containment design specifications. The United States (4,880 reactor-years) and France (2,505 reactor-years) contribute the largest operational datasets. Probabilistic assessments estimate direct DEGB occurrence probabilities with extremely low event frequencies, far below the 10-5/reactor-year thresholds typically used to define non-credible events in nuclear-safety analyses; i.e., events with probability this low fall into beyond-design-basis events. Current material-science knowledge demonstrates that the ductile steel materials used in nuclear piping systems exhibit stable crack-growth behavior fundamentally incompatible with instantaneous severance. International regulatory experience, particularly Germany’s comprehensive break-preclusion implementation, and successful leak-before-break (LBB) applications in almost all of U.S. pressurized water reactor units validate that alternatives can maintain safety performance while reducing economic burden. Current DEGB protection systems impose estimated lifetime costs of hundreds of millions of dollars per unit, over the life of a plant across the nuclear industry (including ongoing costs), representing substantial resource allocation toward scenarios with extremely low probability. Although this report acknowledges uncertainties regarding long-term aging effects, potential synergistic degradation mechanisms, and site-specific seismic considerations that warrant continued evaluation as regulatory policy evolves, there remains no documented evidence that a DEGB has occurred as a consequence of the conditions or mechanisms described in this report. This report acknowledges the Nuclear Regulatory Commission’s (NRC’s) recent efforts—outlined in the draft Interim Staff Guidance (ISG) NRC-DSS-ISG-2025-XX (“Treatment of Certain Loss-of-Coolant Accident Locations as Beyond-Design-Basis Accidents Draft Interim Staff Guidance”)—to reduce overly conservative requirements for large-break loss of coolant accidents through technical justifications and exemptions. However, extensive operating experience and validated methodologies—such as LBB and in-service inspection programs—demonstrate that the probability of a DEGB in reactor coolant-loop piping is extremely low, even under seismic conditions. The authors and reviewers of this report recommend that DEGB be removed as a design-basis event through formal rulemaking, rather than case-by-case exemptions, to better reflect credible failure modes, align with current data, and align with modern, risk-informed safety analysis.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

A Regulatory Approach to Accelerated Deployment for New Material or Applications in Advanced Reactors

New advanced reactor developers may embark on deploying materials in novel and unique environments where a material’s long-term performance may be in question or unknown. In many cases, sufficient test data may not exist for the material in the desired application, or that no prescript or applicable regulatory testing requirements are available to demonstrate the safety of the application explicitly. This study endeavors to develop the framework for a regulatory and technical approach for safe and predictable accelerated materials use in advanced reactors guided by 10 CFR Part 50.43(e)(1), Advanced Reactor Design Criteria contained in Regulatory Guide 1.232, and Reliability Integrity Management Program (RIM) principles.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Promoting the regulatory acceptance of combined ion and neutron irradiation for material degradation in nuclear reactors

The Advanced Materials and Manufacturing Technologies (AMMT) program within the Department of Energy (DOE) Office of Nuclear Energy has developed its current recommendation for promoting the use of combined ion irradiation and neutron irradiation for the accelerated qualification of materials to be deployed in nuclear reactors. This plan is intended to provide a collaborative path forward that can be adopted by academia, national laboratories, and industry, and has been developed with input from the regulatory research arm of the U.S. Nuclear Regulatory Commission (NRC). To deploy new materials or materials manufactured with new technologies, such as additive manufacturing, materials must be evaluated for reactor-induced degradation from the combination of harsh temperatures, corrosive environments, and radiation fields. However, rapid deployment of materials necessitates accelerated testing methods rather than relying on years of neutron irradiation in a material test reactor. Ion irradiation has demonstrated success in reproducing material microstructure and select property evolution resulting from neutron irradiation with three to four orders of magnitude reduction in time and cost, making it an ideal candidate for accelerated irradiation testing. This presentation provides context governing both the scientific and regulatory aspects of the proposed goal. The discussion is aimed at a broad audience including researchers from industry, national laboratories, and academia. The recommended path forward is presented as a conceptual framework of specific steps. In brief, the strategy entails developing an integrated ion and neutron irradiation test plan for the material property of interest based on the fundamental tenet of the linkage of microstructure and properties in materials. Physics-based modeling interprets ion irradiation data and predicts neutron irradiation microstructure and properties with uncertainty bounds. The first round of testing is sufficient for an initial licensing application using a risk-informed approach, while a minimum required neutron irradiation test plan reduces cost and time requirements. A surveillance program with witness specimens in-reactor provides additional data over time to improve model predictions to higher damage levels and further reduce uncertainty bounds, which can be used for license extensions or longer lifetimes in new license applications.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Scaling open-weight large language models for hydropower regulatory information extraction: A systematic analysis

Information extraction from regulatory and technical documents using large language models (LLMs) involves practical trade-offs between extraction quality and computational cost. We evaluate eight open-weight LLMs spanning 0.6B–70B parameters on hydropower licensing documents and report deployment-oriented evidence under a unified extraction schema and evaluation protocol. Across the model set, we observe clear scale-dependent trends in both baseline extraction quality and the effectiveness of reflective reasoning (self-checking) under our fixed-prompt, no-augmentation setting. Mid-scale models often provide a favorable balance of accuracy and efficiency, whereas the smallest models show limited or inconsistent gains from the reasoning variants tested. Larger models achieve the highest overall F1 scores but incur substantially greater compute and infrastructure requirements. We further find that reliability failure modes can distort conventional metrics in this domain: in particular, high recall can coincide with systematic extraction errors when models fabricate values for fields that are absent from the source text, underscoring the importance of conservative null handling and evidence-grounded evaluation. Overall, our study provides a reproducible resource–performance comparison for open-weight LLM-based extraction in hydropower regulatory documentation and offers practical guidance for model selection under different deployment constraints.

Evaluation protocol↗
DOE OSTI2025

Non-LWR Regulatory Framework Modernization- Fiscal Year 2024

This report provides an end-of-year summary that reflects the progress and status of Idaho National Laboratory’s (INL’s) activities concerning the development of an advanced-reactor regulatory framework and its implementation in the United States (U.S.). The report also provides recommendations for work to be performed in Fiscal Year (FY)-25 and beyond. This work was completed in FY-24 and was supported by the U.S. Department of Energy (DOE) Regulatory Development sub-program. These activities are managed by INL on behalf of DOE.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

AquaPV: Regulatory and Environmental Considerations for Floating Photovoltaic Projects Located on Federally Controlled Reservoirs in the United States

To meet the nation's decarbonization goals, the U.S. Department of Energy's Solar Futures study forecasts that installed solar photovoltaic (PV) capacity must increase nearly tenfold, from 80 gigawatts (GW) in 2020 to approximately 760 GW cumulative installed capacity by 2035. Ground-mounted PV is expected to dominate future solar deployment and will require more than 3.5 million acres of land to meet annual demand projections (of nearly 45 GW) by 2030. However, various competing demands for land (e.g., agricultural production, conservation) and high land acquisition costs in specific locations could be challenges to meeting future PV demand solely with ground-mounted PV deployment. Floating photovoltaics (FPV) may be an alternative in locations where ground-mounted PV is not feasible and aid in reaching the nation's PV deployment and decarbonization goals. FPV is a newer siting approach in which a PV array is affixed to a floating apparatus and sited on a water body like a reservoir behind a dam. FPV systems may be stand-alone or co-located at new or existing hydroelectric facilities or pumped storage hydropower (PSH) facility reservoirs. Co-located FPV systems may or may not be operationally paired and work in tandem with the hydroelectric or PSH facility. This report provides novel analysis to understand the opportunities and challenges associated with developing stand-alone and co-located FPV projects on reservoirs in the United States. Specifically, the report explores potential environmental and energy benefits and environmental impacts associated with the siting, construction, and operation of FPV projects. The report also identifies and analyzes U.S. federal- and state-issued permits and authorizations required by federal laws to understand the licensing pathways and regulatory requirements for FPV projects sited on reservoirs licensed by the Federal Energy Regulatory Commission and on powered and non-powered reservoirs owned by the Bureau of Reclamation or U.S. Army Corps of Engineers.

ENERGY PLANNING, POLICY, AND ECONOMY,SOLAR ENERGY↗