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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs

Abstract T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis

Abstract YEASTRACT+ (http://yeastract-plus.org/) is a tool for the analysis, prediction and modelling of transcription regulatory data at the gene and genomic levels in yeasts. It incorporates three integrated databases: YEASTRACT (http://yeastract-plus.org/yeastract/), PathoYeastract (http://yeastract-plus.org/pathoyeastract/) and NCYeastract (http://yeastract-plus.org/ncyeastract/), focused on Saccharomyces cerevisiae, pathogenic yeasts of the Candida genus, and non-conventional yeasts of biotechnological relevance. In this release, YEASTRACT+ offers upgraded information on transcription regulation for the ten previously incorporated yeast species, while extending the database to another pathogenic yeast, Candida auris. Since the last release of YEASTRACT+ (January 2020), a fourth database has been integrated. CommunityYeastract (http://yeastract-plus.org/community/) offers a platform for the creation, use, and future update of YEASTRACT-like databases for any yeast of the users’ choice. CommunityYeastract currently provides information for two Saccharomyces boulardii strains, Rhodotorula toruloides NP11 oleaginous yeast, and Schizosaccharomyces pombe 972h-. In addition, YEASTRACT+ portal currently gathers 304 547 documented regulatory associations between transcription factors (TF) and target genes and 480 DNA binding sites, considering 2771 TFs from 11 yeast species. A new set of tools, currently implemented for S. cerevisiae and C. albicans, is further offered, combining regulatory information with genome-scale metabolic models to provide predictions on the most promising transcription factors to be exploited in cell factory optimisation or to be used as novel drug targets. The expansion of these new tools to the remaining YEASTRACT+ species is ongoing.

Teixeira, Miguel Cacho (ORCID:0000000256766174)↗
DOE OSTI2023

A riboswitch separated from its ribosome-binding site still regulates translation

Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10–G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch—akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Heritable, multinucleotide deletions in plants using viral delivery of a repair exonuclease and guide RNAs

Abstract CRISPR/Cas9-mediated mutagenesis typically results in short insertion/deletion mutations, which are often too small to disrupt the function of cis-acting regulatory elements. Here, we describe a highly efficient in planta gene editing approach called VirTREX2-HLDel that achieves heritable multinucleotide deletions in both protein-coding genes and noncoding DNA regulatory elements. VirTREX2-HLDel uses RNA viruses to deliver both the 3 prime repair exonuclease 2 (TREX2) and single-guide RNAs. Our method enables recovery of multiplexed heritable deletions and increases the heritable gene editing frequency at poorly edited sites. We identified functional conservation and divergence of MICRORNA164 (miR164) in Nicotiana benthamiana and tomato (Solanum lycopersicum) using VirTREX2-HLDel and observed previously uncharacterized phenotypes in plants with large deletions at this locus. Our viral delivery method reduces the need for tissue culture and will accelerate the understanding of protein-coding and regulatory regions in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Commercial Building Planning and Retrofitting Strategy for Grid Services

The increasing integration of distributed energy resources (DERs) plays an important role in improving energy consumption efficiency. In September 2020, the Federal Energy Regulatory Commission (FERC) approved Order 2222 which opens wholesale electricity markets to small capacity DERs. The benefit of this new FERC Order 2222 is that DERs, such as rooftop solar panels and batteries, will be able to participate in regional electricity markets and provide grid services. Meanwhile, the planning and operation strategies of DERs are facing new challenges to account for the impact of the wholesale market with numerous uncertainty factors. Therefore, in this paper, we propose a new planning and retrofitting model for long-term commercial buildings that considers both DER investment and market participation. Specifically, we explore the capability of implementing DERs for grid services. The effectiveness of the proposed model is validated using real-world data. Simulation results also validate that participating in grid services can significantly increase revenues through appropriate building energy management and shorten the payback period of DER investments.

building energy management↗
DOE OSTI2024

PagMYB128 regulates secondary cell wall formation by direct activation of cell wall biosynthetic genes during wood formation in poplar

The biosynthesis of cellulose, lignin, and hemicelluloses in plant secondary cell walls (SCWs) is regulated by a hierarchical transcriptional regulatory network. Here, this network features orthologous transcription factors shared between poplar and Arabidopsis, highlighting a foundational similarity in their genetic regulation. However, knowledge on the discrepant behavior of the transcriptional-level molecular regulatory mechanisms between poplar and Arabidopsis remains limited. In this study, we investigated the function of PagMYB128 during wood formation and found it had broader impacts on SCW formation compared to its Arabidopsis ortholog, AtMYB103. Transgenic poplar trees overexpressing PagMYB128 exhibited significantly enhanced xylem development, with fiber cells and vessels displaying thicker walls, and an increase in the levels of cellulose, lignin, and hemicelluloses in the wood. In contrast, plants with dominant repression of PagMYB128 demonstrated the opposite phenotypes. RNA sequencing and reverse transcription – quantitative polymerase chain reaction showed that PagMYB128 could activate SCW biosynthetic gene expression, and chromatin immunoprecipitation along with yeast one-hybrid, and effector–reporter assays showed this regulation was direct. Further analysis revealed that PagSND1 (SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN1) directly regulates PagMYB128 but not cell wall metabolic genes, highlighting the pivotal role of PagMYB128 in the SND1-driven regulatory network for wood development, thereby creating a feedforward loop in SCW biosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

F‐Box Protein‐Mediated Proteolytic Regulation of Phenylpropanoid Metabolism in Response to Biotic and Abiotic Stresses

Protein ubiquitination is a central regulatory mechanism governing plant growth, development and environmental adaptation. Ubiquitylomic studies have revealed that many enzymes in phenylpropanoid biosynthetic pathways are subject to ubiquitination. Increasing evidence indicates that specific F-box proteins target key enzymes in these pathways, including PAL, CCR, CAD, COMT and peroxidases in the lignin biosynthetic branch, and CHS in the flavonoid biosynthetic branch, thereby promoting their ubiquitination and selective degradation. These F-box proteins act in response to diverse developmental and environmental cues, including cellular carbon status, light quality and intensity, and biotic stresses (e.g., pathogen and insect attack). By regulating the stability and activity of both enzymes and regulatory proteins involved in phenylpropanoid biosynthesis, F-box proteins modulate the accumulation of simple phenolics and lignin polymers, ultimately contributing to plant resilience. This review summarizes recent advances in the characterization of F-box proteins involved in phenylpropanoid metabolism and their regulatory roles in response to biotic and abiotic stresses and identifies key knowledge gaps that limit mechanistic understanding of F-box protein-mediated proteolytic regulation of phenylpropanoid metabolism. In conclusion, insights into ubiquitin-mediated proteolytic control of phenylpropanoid metabolism offer promising avenues for enhancing bioactive phenolic production, advancing biofuel feedstock engineering and improving crop stress tolerance.

(A)biotic stress↗
DOE OSTI2020

A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR

Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large–scale systems–level analysis of the protein–DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high–throughput enhanced yeast one–hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis–regulatory elements (CREs) in ER stress–responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Lastly, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription–regulatory mechanisms in the stress responses and crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Xylanolytic metabolism is regulated by coordination of transcription factors XynR and XylR in extremely thermophilic Caldicellulosiruptorales

ABSTRACT Global transcription factors (TFs) control metabolic processes in bacteria to efficiently utilize available carbon. The orderCaldicellulosiruptoraleshas drawn interest due to the ability of its members to degrade components of lignocellulosic biomass. Regulatory reconstruction ofAnaerocellum (f. Caldicellulosiruptor) besciiidentified two major global transcription factors for xylan utilization, XynR and XylR, and the corresponding putative transcription factor binding sites. Recombinant versions of XynR (LacI family) and XylR (ROK family) were subjected to fluorescence polarization (FP) and biolayer interferometry (BLI) analysis to confirm the predicted binding sites. Four XynR sites and two XylR sites were validated, accounting for 20 of 26 genes regulated by XynR and six of seven genes regulated by XylR. Bioinformatic analysis of the individual genes controlled by the two regulators showed an inter-dependent scheme for xylan conversion; the transport of xylooligosaccharides (XOS) is dependent on XylR, while enzymes responsible for hydrolysis are controlled by both regulators. For xylose catabolism by the xylose isomerase-xylulose kinase pathway, regulation is also split, with XylR controlling xylose isomerase and XynR controlling xylokinase. The XynR/XylR regulator pair withinA. besciiis conserved in all sequenced species ofCaldicellulosiruptorales, suggesting similarities in regulating linear xylan conversion. In other xylanolytic thermophiles, XylR homologs control xylan degradation, compared to just 6 out of 26 genes forA. bescii. These results show that two separate regulatory schemes (dual repression) are coordinated byA. besciito effectively regulate the hemicellulose inventory and xylan catabolism. IMPORTANCE To take full advantage of extreme thermophiles as platform metabolic engineering microorganisms, the tools for genetic manipulation must be further developed, and strategies that exploit a better understanding of metabolic regulation need to be discerned.Anaerocellum bescii, the most studied of the extremely thermophilic fermentative anaerobic bacteria that can utilize microcrystalline cellulose, can degrade microcrystalline cellulose and hemicellulose and has been metabolically engineered to convert the resulting sugars to products such as ethanol and acetone. For xylan, in particular, two major global transcription factors (TFs), XynR and XylR, play a role in sugar metabolism, although their predicted regulatory interdependence from bioinformatics analysis has not been elucidated experimentally. Here, fluorescence polarization (FP) and biolayer interferometry (BLI) were used to explore this issue to support metabolic engineering efforts aimed at improving carbohydrate processing to industrial chemicals.

Biotechnology & Applied Microbiology↗
DOE OSTI2020

Tailoring a Global Iron Regulon to a Uropathogen

Pathogenicity islands and plasmids bear genes for pathogenesis of various Escherichia coli pathotypes. Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here, we dissected a regulatory network directed by the conserved iron homeostasis regulator, ferric uptake regulator (Fur), in uropathogenic E. coli (UPEC) strain CFT073. Comparing anaerobic genome-scale Fur DNA binding with Fur-dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655 showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O 2 -dependent synthesis of the siderophore aerobactin, encoded by an operon within a pathogenicity island. Taken together, these data suggest that in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O 2 to produce aerobactin. IMPORTANCE Host iron restriction is a common mechanism for limiting the growth of pathogens. We compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E. coli K-12 to uncover strategies that pathogenic bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important in controlling growth and survival under nutrient-limiting conditions and during transitions from the nutrient-rich environment of the lower gastrointestinal (GI) tract to the more restrictive environment of the urinary tract. The coupling of the response of iron limitation to increased demand for amino acids could be a critical attribute that sets UPEC apart from other E. coli pathotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗
DOE OSTI2024

Drug providers’ perspectives on antibiotic misuse practices in eastern Ethiopia: a qualitative study

Objective Antibiotic misuse includes using them to treat colds and influenza, obtaining them without a prescription, not finishing the prescribed course and sharing them with others. Although drug providers are well positioned to advise clients on proper stewardship practices, antibiotic misuse continues to rise in Ethiopia. It necessitates an understanding of why drug providers failed to limit such risky behaviours. This study aimed to explore drug providers’ perspectives on antibiotic misuse practices in eastern Ethiopia. Setting The study was conducted in rural Haramaya district and Harar town, eastern Ethiopia. Design and participants An exploratory qualitative study was undertaken between March and June 2023, among the 15 drug providers. In-depth interviews were conducted using pilot-tested, semistructured questions. The interviews were transcribed verbatim, translated into English and analysed thematically. The analyses considered the entire dataset and field notes. Results The study identified self-medication pressures, non-prescribed dispensing motives, insufficient regulatory functions and a lack of specific antibiotic use policy as the key contributors to antibiotic misuse. We found previous usage experience, a desire to avoid extra costs and a lack of essential diagnostics and antibiotics in public institutions as the key drivers of non-prescribed antibiotic access from private drug suppliers. Non-prescribed antibiotic dispensing in pharmacies was driven by client satisfaction, financial gain, business survival and market competition from informal sellers. Antibiotic misuse in the setting has also been linked to traditional and ineffective dispensing audits, inadequate regulatory oversights and policy gaps. Conclusion This study highlights profits and oversimplified access to antibiotics as the main motivations for their misuse. It also identifies the traditional antibiotic dispensing audit as an inefficient regulatory operation. Hence, enforcing specific antibiotic usage policy guidance that entails an automated practice audit, a responsible office and insurance coverage for persons with financial limitations can help optimise antibiotic use while reducing resistance consequences.

General & Internal Medicine↗
DOE OSTI2024

Ecological Benchmark for Chemicals

The Ecological Benchmark Tool dataset serves as a comprehensive repository of benchmarks designed to assess ecological risks at contaminated sites. This tool facilitates the evaluation of various environmental media and contaminants, supporting regulatory compliance and ecological protection. Benchmarks are available for air, biota, sediment, soil, and surface water. The dataset also provides species-specific benchmarks for fish, plants, birds, mammals, and invertebrates. Users can select benchmark sources, media, individual chemicals, and retrieve results in tabular or spreadsheet formats for analysis. Benchmarks are derived from authoritative sources, including government agencies, scientific councils, and academic publications. The dataset supports ecological risk assessments, regulatory decision-making, and environmental planning, with tools for benchmarking against chemical thresholds, sensitive species protection, and habitat impact evaluations. This structured approach ensures a robust evaluation of ecological risks tailored to site-specific and regulatory needs.

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

Ecological Benchmark for Radionuclides

The Ecological Benchmark Tool for radionuclides dataset serves as a comprehensive repository of benchmarks designed to assess ecological risks at contaminated sites. This tool facilitates the evaluation of various environmental media and contaminants, supporting regulatory compliance and ecological protection. Benchmarks are available for sediment, soil, and surface water. The dataset also provides species-specific benchmarks for fish, plants, birds, mammals, and invertebrates. Users can select benchmark sources, media, individual radionuclides, and retrieve results in tabular or spreadsheet formats for analysis. Benchmarks are derived from authoritative sources, including government agencies, scientific councils, and academic publications. The dataset supports ecological risk assessments, regulatory decision-making, and environmental planning, with tools for benchmarking against radiological thresholds, sensitive species protection, and habitat impact evaluations. This structured approach ensures a robust evaluation of ecological risks tailored to site-specific and regulatory needs.

Stewart, Debra [Oak Ridge National Laboratory (ORN↗
DOE OSTI2021

Optimal dimensionality selection for independent component analysis of transcriptomic data

Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independent component analysis effectively reveals both the source signals of the transcriptome as co-regulated gene sets, and the activity levels of the underlying regulators across diverse experimental conditions. Two major variables that affect the final gene sets are the diversity of the expression profiles contained in the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question. We computed independent components across a range of dimensionalities for four gene expression datasets with varying dimensions (both in terms of number of genes and number of samples). We computed the correlation between independent components across different dimensionalities to understand how the overall structure evolves as the number of user-defined components increases. We then measured how well the resulting gene clusters reflected known regulatory mechanisms, and developed a set of metrics to assess the accuracy of the decomposition at a given dimension. We found that over-decomposition results in many independent components dominated by a single gene, whereas under-decomposition results in independent components that poorly capture the known regulatory structure. From these results, we developed a new method, called OptICA, for finding the optimal dimensionality that controls for both over- and under-decomposition. Specifically, OptICA selects the highest dimension that produces a low number of components that are dominated by a single gene. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes. OptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Learning genetic perturbation effects with variational causal inference

Advances in sequencing technologies have enhanced the understanding of gene regulation in cells. In particular, Perturb-seq has enabled high-resolution profiling of the transcriptomic response to genetic perturbations at the single-cell level. This understanding has implications in functional genomics and potentially for identifying therapeutic targets. Various computational models have been developed to predict perturbational effects. While deep learning models excel at interpolating observed perturbational data, they tend to overfit in the lack of enough data and may not generalize well to unseen perturbations. In contrast, mechanistic models, such as linear causal models based on gene regulatory networks, hold greater potential for extrapolation, as they encapsulate regulatory information that can predict responses to unseen perturbations. However, their application has been limited to small studies due to overly simplistic assumptions, making them less effective in handling noisy, large-scale single-cell data. We propose a hybrid approach that combines a mechanistic causal model with variational deep learning, termed Single Cell Causal Variational Autoencoder (SCCVAE). The mechanistic model employs a learned regulatory network to represent perturbational changes as shift interventions that propagate through the learned network. SCCVAE integrates this mechanistic causal model into a variational autoencoder, generating rich, comprehensive transcriptomic responses. Our results indicate that SCCVAE exhibits superior performance over current state-of-the-art baselines for extrapolating to predict unseen perturbational responses. Additionally, for the observed perturbations, the latent space learned by SCCVAE allows for the identification of functional perturbation modules and simulation of single-gene knockdown experiments of varying penetrance, presenting a robust tool for interpreting and interpolating perturbational responses at the single-cell level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Development of Dry Cask Risk Tools

The Nuclear Regulatory Commission (NRC) has repeatedly expressed a desire to increase the use of risk in its decision-making. The Probabilistic Risk Assessment (PRA) Policy Statement published in 1995 formalized the Commission’s commitment to risk-informed regulation through the expanded use of PRA. While a great deal of work has been done to incorporate risk insights into the regulatory framework for at-power nuclear reactors. Far less progress has been made to risk inform the dry-casks and nuclear waste transportation areas of the nuclear fuel cycle. INL was tasked with incorporating the information from the two completed dry cask PRAs as well as any additional available information into a tool that helps the NRC use those insights to identify levels of risk at various stages in the nuclear waste cycle. The first task was to address the License Amendment Request (LAR) Process for Dry Cask storage, the second task is for the incorporate transportation into the tool, and the third and final task will be incorporate any additional regulatory applications for dry cask storage. This report covers the first task of the tool and will eventually incorporate the remaining two tasks may be completed in the future and built off the model described here. Task 1 specifically asked to incorporate the risk insights into the process for determining and prioritizing review of license amendment changes related to storage applications by outlining a resource allocation strategy and defining recommendations of for the depth and breadth of the LAR review. It was requested that the tool be similar in design to the SDP notebooks/worksheets and contain quantitative, qualitative, or semi-quantitative approaches to assessing the risk of the change. The final tool that was selected by INL to be developed was a flowchart and associated rationale document that allows the reviewer to quickly assess potential LAR changes and their associated risks as well as the rationale behind the risk categorization. This risk categorization will lead to specific actionable recommendations to expect from a change of that specific category. This allows for a more consistent review process as well as improving the overall efficiency of the review itself.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2020

Model MC&A for Pebble Bed Reactors (Technical Direction No. 5 Task 2.6 Letter Report)

In preparation for non-light water reactor (non-LWR) activities, US Nuclear Regulatory Commission (NRC) staff are advancing risk-informed and performance-based licensing approaches and addressing key policy issues. One non-LWR reactor concept is a pebble bed reactor (PBR). This reactor design uses spherical fuel elements (pebbles) that are continually added to and removed from the reactor core. The free movement of the fuel in this design presents new challenges for material control and accounting (MC&A) programs. Therefore, an assessment of MC&A program features and measures for a PBR was performed to help NRC staff develop associated MC&A regulations or regulatory guides. The current regulatory framework for non-LWR fuel cycles excludes support for licensing reviews for MC&A programs for PBRs. Licensing reviews of an MC&A program for PBRs can be facilitated by (1) a model MC&A program for a PBR based on identification and assessment of MC&A program features and recommended measures for a reference PBR and (2) a methodology for assessing MC&A performance that can help assess different MC&A program features and measures. This report supports the NRC’s non-LWR Vision and Strategy Near-Term Implementation Action Plans.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗