Developmental Assessment and Verification and Validation of RELAP5-3D
Presentation on work completed on RELAP5-3D developmental assessment and verification and validation documentation processes.
22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
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Assessing the Ability of Developmentally Precocious Estrogen Signaling to Recapitulate Ovarian Transcriptomes and Follicle Dynamics in Alligators from a Contaminated Lake
Concern has grown in recent decades over anthropogenic contaminants that interfere with the functioning of endocrine hormones. However, mechanisms connecting developmental processes to pathologies associated with endocrine-disrupting chemical (EDC) exposure are poorly understood in naturally exposed populations. We sought to a) characterize divergence in ovarian transcriptomic and follicular profiles between alligators originating from a historically EDC-contaminated site, Lake Apopka, and a reference site; b) test the ability of developmentally precocious estrogen exposure to recapitulate site-associated patterns of divergence; and c) test whether treatment with exogenous follicle-stimulating hormone (FSH) is capable of rescuing phenotypes associated with contaminant exposure and/or embryonic estrogen treatment. Alligators eggs were collected from a contaminated site and a reference site, and a subset of eggs from the reference site were treated with estradiol (E2) during embryonic development prior to gonadal differentiation. After hatching, alligators were raised under controlled laboratory settings for 5 months. Juveniles from both sites were divided and treated with exogenous FSH. Histological analyses and RNA-sequencing were conducted to characterize divergence in ovarian follicle dynamics and transcriptomes between sites, between reference and E2-treated animals, and between FSH-treated and nontreated animals. We observed broad site-of-origin divergence in ovarian transcriptomes and reductions in ovarian follicle density between juvenile alligators from Lake Apopka and the reference site. Treating embryos from the reference site with E2 overwhelmingly recapitulated transcriptional and histological alterations observed in Lake Apopka juveniles. Ovarian phenotypes observed in Lake Apopka alligators or resulting from estrogen treatment were only partially rescued by treatment with exogenous FSH. Recapitulation of ovarian abnormalities by precocious E2 revealed a relatively simple mechanism underlying contaminant-induced pathologies in a historical example of environmental endocrine disruption. Findings reported here support a model where the developmental timing of estrogen signaling has the potential to permanently alter ovarian organization and function.
59 BASIC BIOLOGICAL SCIENCES↗
Corrosion Behavior of Developmental Iron Phosphate Waste Forms: FY20 Status Report
Corrosion tests were performed to assess the dissolution behaviors of developmental iron phosphate materials that are being evaluated as an alternative to the glass-bonded sodalite ceramic waste form to immobilize salt wastes from electrochemical separation operations. Production of the iron phosphate waste form results in dehalogenation of the waste salt that increases potential waste loading. Ferric oxide is added to the waste form to increase the chemical durability. Tests conducted to optimize the amount of ferric oxide used to make the waste form are summarized in this report. Specimens prepared from materials made with between 17 and 34 mole % ferric oxide were subjected to two test methods to assess the effects of the iron content on the relative durability and retention of immobilized salt cations including cesium, strontium, and neodymium. Modified ASTM C1308 test results show the intrinsic durability was significantly higher for materials made with 27 mol % ferric oxide. Further additions generated iron-rich inclusion phases and did not improve durability. Modified ASTM C1285 test results show that solution feedback attenuates the dissolution rate similar to what is observed for borosilicate glasses within seven days. Analyses of test specimens after 42 days show no evidence that surface layers formed. Combined with previous studies addressing the salt loading, a composition region of the ammonium (di)hydrogen phosphate-waste salt-ferric oxide ternary has been defined for durable waste form compositions. Materials with that composition can be used to determine optimal processing conditions, assess long-term performance, and parameterize a degradation model.
Stariha, S. A.↗
Methodology for Estimating Performance and Cost of Natural Gas Combined Cycle Plants with Carbon Capture
This document describes a methodology that allows developers and evaluators to assess the status of developmental, natural gas combined cycle (NGCC) power plant post-combustion carbon dioxide (CO 2 ) separation technologies with respect to NETL performance and cost metrics. Developmental CO 2 separation technologies that might apply for NGCC post-combustion power generation can be placed into several categories, including, but not limited to membranes, solvents, sorbents, adsorbents, and phase-change technologies. The intent of this product is to provide a consistent methodology for high-level comparison of in-development technology to a standardized baseline.
20 FOSSIL-FUELED POWER PLANTS↗
Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
Single-cell genomics permits a new resolution in the examination of molecular and cellular dynamics, allowing global, parallel assessments of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the light–dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced, plant, the semiaquaticWolffia australiana, to understand dynamics of cell expression in these contexts at the whole-plant level. We examined single-cell-resolution RNA-sequencing data and foundWolffiacells divide into four principal clusters representing the above- and below-water-situated parenchyma and epidermis. Although these tissues share transcriptomic similarity with model plants, they display distinct adaptations thatWolffiahas made for the aquatic environment. Within this broad classification, discrete subspecializations are evident, with select cells showing unique transcriptomic signatures associated with developmental maturation and specialized physiologies. Assessing this simplified biological system temporally at two key time-of-day (TOD) transitions, we identify additional TOD-responsive genes previously overlooked in whole-plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in cell-specific manners, even in this simplified system. Distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of unexpectedly few genes, characterizingWolffiaas a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes.Wolffiaprovides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.
Biochemistry & Molecular Biology↗
Evaluating Climate Models’ Cloud Feedbacks Against Expert Judgment
Abstract The persistent and growing spread in effective climate sensitivity (ECS) across global climate models necessitates rigorous evaluation of their cloud feedbacks. Here we evaluate several cloud feedback components simulated in 19 climate models against benchmark values determined via an expert synthesis of observational, theoretical, and high‐resolution modeling studies. We find that models with smallest feedback errors relative to these benchmark values generally have moderate total cloud feedbacks (0.4–0.6 W m −2 K −1 ) and ECS (3–4 K). Those with largest errors generally have total cloud feedback and ECS values that are too large or too small. Models tend to achieve large positive total cloud feedbacks by having several cloud feedback components that are systematically biased high rather than by having a single anomalously large component, and vice versa. In general, better simulation of mean‐state cloud properties leads to stronger but not necessarily better cloud feedbacks. The Python code base provided herein could be applied to developmental versions of models to assess cloud feedbacks and cloud errors and place them in the context of other models and of expert judgment in real‐time during model development.
58 GEOSCIENCES↗
Corrosion rates measured under potentiostatic conditions to represent performance of a cermet nuclear waste form
Electrochemical tests were conducted to assess the corrosion performance of a developmental multiphase cermet nuclear waste form in different conditions. Corrosion currents were monitored as the surface equilibrated in an acidic brine solution during potentiostatic tests at different imposed potentials. Electrochemical impedance spectroscopy was used to quantify differences in the electrical properties of surfaces stabilised at different potentials. The passivating oxides that will stabilise the surface under disposal conditions are formed and maintained during testing. The measured corrosion currents were two orders of magnitude lower for passivated surfaces than for polished surfaces over a wide range of redox conditions. The electrochemical results were correlated with microscopic analyses of the corroded surfaces and physical models of the surface passivation and degradation processes are proposed. The measured corrosion rates are suitable for the long-term performance modeling of cermet nuclear waste forms.
Gattu, V. K.↗
Uncertainty Quantification of Machine Learning Predicted Creep Property of Alumina-Forming Austenitic Alloys
The development of machine learning (ML) approaches in materials science offers the opportunity to exploit existing engineering and developmental alloy datasets, such as Oak Ridge National Laboratory (ORNL)’s consistently measured creep-rupture dataset for alumina-forming austenitic (AFA) alloys, to accelerate their further development. As a first step toward achieving ML insights for improved alloy design, the potential sources of uncertainty and their impacts on ML output are examined. It is observed that the selection of algorithms and features as well as data sampling significantly affects the performance of ML models, either positively or negatively. Further, the performance of various ML models in predicting the creep properties of AFA alloys is compared, with further evaluation by assessment of a small set of new developmental AFA alloys that were not part of the training dataset. The present study demonstrates that uncertainty quantification (UQ) is essential in materials science for evaluating the performance of ML algorithms with specifically selected feature sets and obtaining a comprehensive understanding of their limitations and the resultant capability of effective prediction in complex materials systems.
36 MATERIALS SCIENCE↗
Early Inference of Nuclear Technology-Directed Research Activities of Authors from Scientific Publications
Nuclear research articles can provide information about early nuclear proliferation indicators such as influential research entities and technology capability levels of a country, but detection of nuclear activities typically occurs after they have started. We investigate the extent to which nuclear research articles can be used to infer whether a research entity will acquire or develop a nuclear technology before it happens. Early detection of nuclear proliferation or technology development indicators from data is challenging due to partial observability, sparse and unlabeled information, and confounding signals from multiple concurrent activities. This paper presents the early detection problem as a sequential decision-making, goal inference problem, where the objective is to characterize and predict an individual’s, organization’s, or a country’s intent (unobserved goal-directed behavior) towards developing a nuclear capability from partially observed sequences of their research publications, using inverse reinforcement learning and Bayesian goal inference methods. A computational framework is presented, and its application demonstrated using 29,196 Scopus records for a case study related to a civil nuclear capability. The case study results serve as a proof-of-concept demonstration for inference of technology-directed research activity of authors who publish in the nuclear domain. The inference method, combined with advanced computing, may be used to assess and monitor activities pertaining to early developmental stages of a nuclear technology or capability, which in turn can help to identify and prioritize activities with nuclear proliferation potential for further investigation.
98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
A microfluidic spore chamber for long-term imaging of single-spore hyphal development.
Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device's capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, and stress-associated phenomena such as microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host–microbe interaction research.
Antifungal screening↗
Dataset for "A Microfluidic Spore Chamber for Long-Term Imaging of Single-Spore Hyphal Development"
Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device’s capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host–microbe interaction research. Videos of the observed phenomena are included in this data set.
59 BASIC BIOLOGICAL SCIENCES↗
Feasibility of carbon foam-based sorbents for the abatement of gaseous mercury and iodine
The U.S. Department of Energy Hanford Site in Washington State is in the process of commissioning the Waste Treatment and Immobilization Plant to process a portion of the 54 million gallons of radioactive and chemical waste from cold war weapon production. Technologies for the capture of volatile species of concern are still being assessed, and new methods and materials are developed as operational and flowsheet mission risks are identified. One such area still being assessed is the abatement efficacy of the Carbon Adsorber units to retain gaseous mercury and 129 I released during processing. It is challenging to predict the mercury chemistry due to the variability of the feed, and different methods/materials are required for the capture of gaseous Hg 0 and Hg II compounds. In this study, the feasibility of using developmental carbon foam (CF) sorbents for the capture of iodine and mercury was assessed using static and dynamic flow testing and compared against a commercially available sorbent, BATII-37. Both CF and CF functionalized with bismuth particles (CF-Bi) chemisorbed iodine, and CF-Bi had similar mercury capture performance to BATII-37 in dynamic flow tests. While species loading concentrations were measurable, limitations in achieving a mass balance prevented a full evaluation of capture efficacy. Nonetheless, the results serve as an important first step in demonstrating the potential for simultaneous iodine and mercury capture.
Hanford site↗
Uncovering hidden enhancers through unbiased in vivo testing
Chromatin signatures are widely used to identify tissue-specific in vivo enhancers, but their sensitivity and specificity remains unclear. Here we show that many developmental enhancers remain undetectable using currently available chromatin data. In an initial comparison of over 1200 developmental enhancers with tissue-matched chromatin data, 14% (n = 285) lacked canonical enhancer-associated chromatin signatures. To further assess the prevalence of enhancers missed by chromatin profiling approaches, we used a high-throughput transgenic enhancer assay to screen the regulatory landscapes of two key developmental genes at 5 kb resolution, spanning 1.3 Mb of mouse sequence in total. We observed that 23 of 88 (26%) in vivo enhancers discovered by this approach lacked enhancer-associated chromatin signatures in the respective tissue. Our findings suggest the existence of tens of thousands of enhancers that remain undiscovered by currently available chromatin data, underscoring the continued need for expanding resources for enhancer discovery.
Epigenomics↗
Virus-induced gene editing of stomatal regulators in Nicotiana benthamiana enables rapid functional genomics
Virus-induced gene editing (VIGE) holds promise as a rapid and scalable approach for functional genomics in plants. Here, we apply a tobacco rattle virus (TRV)-based single-guide RNA (sgRNA) delivery system to target key regulators of stomatal development in Nicotiana benthamiana using transgenic Cas9-expressing lines. sgRNAs fused to a mobile RNA element and co-delivered with TRV enabled both somatic and heritable genome editing across orthologs of STOMAGEN, EPF2, YODA, and SPEECHLESS. Somatic editing frequencies reached up to 95%, and heritable tetra-allelic mutations were recovered in multiple target genes. Mutants exhibited significant, gene-specific changes in stomatal density, with corresponding effects on leaf temperature indicative of altered evaporative cooling. Additionally, sgRNAs fused to an AmCyan reporter enabled visualization of virus-infected tissues, allowing stomatal phenotyping in edited M0 sectors. This TRV-based platform facilitates functional assessment of genes influencing stomatal patterning and offers a powerful tool for dissecting gene function in a developmentally and physiologically relevant context.
60 APPLIED LIFE SCIENCES↗
Intrinsic and extrinsic factors interact during development to influence telomere length in a long‐lived reptile
Abstract The mechanisms connecting environmental conditions to plasticity in biological aging trajectories are fundamental to understanding individual variation in functional traits and life history. Recent findings suggest that telomere biology is especially dynamic during early life stages and has long‐term consequences for subsequent reproduction and survival. However, our current understanding is mostly derived from studies investigating ecological and anthropogenic factors separately, leaving the effects of complex environmental interactions unresolved. American alligators ( Alligator mississippiensis ) are long‐lived apex predators that rely on incubation temperature during a discrete period during development and endocrine cues to determine sex, making them especially vulnerable to current climatic variability and exposure to anthropogenic contaminants interfering with hormone function. Here, we combine field studies with a factorial design to understand how the developmental environment, along with intrinsic biological variation contribute to persistent telomere variation. We found that exposure to a common endocrine disrupting contaminant, DDE, affects telomere length, but that the directionality is highly dependent upon incubation temperature. Variation in hatchling growth, underlies a strong clutch effect. We also assess concentrations of a panel of glucocorticoid hormones and find that contaminant exposure elicits an increase in circulating glucocorticoids. Consistent with emerging evidence linking stress and aging trajectories, GC levels also appear to trend with shorter telomere length. Thus, we add support for a mechanistic link between contaminants and glucocorticoid signalling, which interacts with ecological aspects of the developmental environment to alter telomere dynamics.
Bae, Junsoo↗
Transient Copper Exposure During Embryogenesis and Temperature Affect Developmental Rate, Survival, and Fin Regeneration in Japanese Medaka ( Oryzias latipes )
Combined environmental stressors that an organism experiences can have both immediate and lasting consequences. In this paper we exposed medaka (Oryzias latipes) embryos to sublethal copper sulfate (CuSO 4 ) (0, 10, and 100 ppb) in combination with different rearing temperatures (27, 30, and 33°C) to assess acute and latent effects on development, growth, and regenerative capacity. Embryos exposed to CuSO 4 and/or higher temperatures hatched significantly earlier. At 4 months post-exposure, fish exposed to low levels of CuSO 4 during development had higher survival, while fish exposed to both 100 ppb CuSO 4 and 33°C temperatures had significantly lower survival. Additionally, a sex-specific effect of embryonic CuSO 4 exposure was observed as female mass decreased with increasing copper dose. We also assessed caudal fin regenerative capabilities in both embryo-exposed fish at 4 months of age and adult medaka that were exposed to 0, 10, and 100 ppb CuSO 4 at room temperature during a 14- day trial. Whereas fin regeneration was unaffected by adult exposure to copper, fish transiently exposed during embryogenesis displayed an initial increase in fin growth rate and an increased incidence of abnormal fin morphology following regrowth. Collectively, these data suggest that developmental copper exposure has the potential to exert long lasting impacts to organismal growth, survival, and function.
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes
The OSU/PNNL Superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons (PAHs) at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. Toward this end, we have linked over 150 PAHs found at Superfund sites to the effect of these same chemicals in zebrafish, creating a rich dataset that links environmental exposure to biological response. To quantify this response, we have implemented a dose-response modelling pipeline to calculate benchmark dose parameters which enable potency comparison across over 500 chemicals and 10 zebrafish-specific phenotypes. Our portal provides public access to this dataset via an interactive web site designed to support exploration and re-use of these data by the scientific community at http://srp.pnnl.gov.
Gosline, Sara JC↗
PNNL Superfund Research Program Analytics (srpAnalytics Data Release v.1.0)
The OSU/PNNL superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. The PNNL Superfund have implemented a dose-response modelling pipeline to calculate benchmark dose parameters that enable the comparison of potency across chemicals and phenotypes. Our portal provides public access to this dataset and an interactive web site designed to enable exploration and re-use of this data by the scientific community at http://srp.pnnl.gov.
59 BASIC BIOLOGICAL SCIENCES↗