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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A Complex Interplay between Nitric Oxide, Quorum Sensing, and the Unique Secondary Metabolite Tundrenone Constitutes the Hypoxia Response in Methylobacter

Methylobacter species, members of the Methylococcales, have recently emerged as some of the globally widespread, cosmopolitan species that play a key role in the environmental consumption of methane across gradients of dioxygen tensions. In this work, we approached the question of howMethylobacter copes with hypoxia, via laboratory manipulation. Through comparative transcriptomics of cultures grown under high dioxygen partial pressure versus cultures exposed to hypoxia, we identified a gene cluster encoding a hybrid cluster protein along with sensing and regulatory functions. Through mutant analysis, we demonstrated that this gene cluster is involved in the hypoxia stress response. Through additional transcriptomic analyses, we uncovered a complex interconnection between the NO-mediated stress response, quorum sensing, the secondary metabolite tundrenone, and methanol dehydrogenase functions. This novel and complex hypoxia stress response system is so far unique to Methylobacter species, and it may play a role in the environmental fitness of these organisms and in their cosmopolitan environmental distribution.Here, we describe a novel and complex hypoxia response system in a methanotrophic bacterium that involves modules of central carbon metabolism, denitrification, quorum sensing, and a secondary metabolite, tundrenone. This intricate stress response system, so far unique to Methylobacter species, may be responsible for the persistence and activity of these species across gradients of dioxygen tensions and for the cosmopolitan distribution of these organisms in freshwater and soil environments in the Northern Hemisphere, including the fast-melting permafrosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Uptake, Efflux, and Sequestration of Mercury in the Asian Clam, Corbicula fluminea , at Environmentally Relevant Concentrations, and the Implications for Mercury Remediation

(1) Mercury (Hg) is a persistent, ubiquitous contaminant that readily biomagnifies into higher trophic level species in aquatic environments across the globe. It is crucial to understand the movement of environmentally relevant concentrations of Hg in impacted freshwater streams to minimize risks to ecological and human health. (2) The bioconcentration kinetics of aqueous Hg exposure (20, 100, and 200 ng/L) in the invasive Asian Clam, Corbicula fluminea, were measured. A toxicokinetic model, the first parameterized for Hg accumulation in freshwater clams, was developed to estimate uptake and efflux parameters and compared to previous parameter values estimated for other mollusk species. (3) Results demonstrated that even at low Hg concentrations, Corbicula record signals of contamination through bioconcentration, and both direct measurement and toxicokinetic models demonstrate large Hg bioconcentration factors (as high as 1.34 × 10 5 mL/g dry tissue), similar to partitioning coefficients seen in engineered Hg sorbents. (4) Our study found that Corbicula accumulated Hg at aqueous concentrations relevant to impacted streams, but well below regulatory drinking water limits, demonstrating their utility as a sensitive sentinel species and potential bioremediator.

bioaccumulation↗
DOE OSTI2022

Integration of Control Methods and Digital Twins for Advanced Nuclear Reactors

Advanced nuclear reactors offer a new set of features to energy generation, due to their ability to adapt to variable energy demand, operate autonomously, be deployed in rural locations and monitored remotely, afford compact size and lower power ratings, and rely on novel technologies to achieve safer operations. Thus, a requirement for the success of these reactors is the use of intelligent forms of control to track changing power demands, make autonomous decisions, and reduce the need for human involvement. Regulatory requirements pertaining to control of nuclear reactors could be met via historical means of control; however, these are not expected to enable the level of highly autonomous operations desired in advanced nuclear reactors. Historical control methods rely on both logical and high-performance (HP) control. These two types of control are usually used separately, with a human element being introduced whenever decisions are cascaded from one science to another. AI/ML control, on the other hand, can replace the human element in the current U.S. fleet of nuclear power plants (NPPs) by acting as a supervisory optimizer that understands the plant internal/external variables in order to make control decisions, and can easily handle non-linear and multi-input/multi out (MIMO) decisions—another requirement for advanced nuclear reactors that could be difficult to handle via logical and HP control. Because of the harsh operating environments produced in advanced reactors, resulting in the frequent failure of sensors and other types of equipment, and considering the lack of operating history for advanced nuclear reactors, control of advanced nuclear reactors would necessitate relying on a model that can track and adapt to the actual process (i.e., a digital twin). This digital twin can make approximations when knowledge and data are unavailable and would evolve as more knowledge is gained. The reactor control must also be risk-informed to account for the high-consequence nature of advanced reactors. This report introduces a high-level (i.e., not method- or process-specific) integration of the three different control and digital twinning methods able to meet the requirements for advanced nuclear reactors. These methods could be applied during both the operational and design stages of these reactors. The aim is to demonstrate how each method interfaces with and highlights enabling solutions necessitated by the unique features of advanced nuclear reactors.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Environmental Flow Requirements from FERC Licenses Across the US

Environmental flow requirements included in Federal Energy Regulatory Commission (FERC) hydropower licenses are important for balancing natural properties and benefits of river ecosystems (e.g., healthy species, recreation, water supply, flood control) supporting hydropower production. In some cases, environmental flow requirements may limit operational flexibility given current operational schemes and make a hydropower plant less able to provide power to the electric grid on demand. Hydropower plants may gain some flexibility as hydropower scheduling time periods are made to be more responsive to the short-term needs of an energy grid increasingly reliant on intermittent renewables. However, many flow requirements focus on the daily, monthly, or seasonal flow fluctuations which matches the time scale of most paradigms linking flow alterations to the health of river ecosystems. This dataset seeks to provide a greater understanding of how flexibility in environmental requirements can be leveraged to create positive outcomes for both the power system and the environment. It contains information on environmental flow requirements from the Protection, Mitigation, and Enhancement section of 50 randomly selected FERC licenses: 25 issued from 1998-2013 that were also included in the ORNL Mitigation Database (Schramm et al. 2015) and 25 issued from 2014-present. The information on environmental flow requirements was extracted from the PM&E section of 50 randomly selected FERC licenses: 25 issued from 1998-2013 that were also included in the ORNL Mitigation Database (Schramm et al. 2015) and 25 issued from 2014-present. The flow requirements were then categorized into flow augmentation categories based on whether the license stated a specific water management purpose for the given requirement called augmentation categories (i.e., fisheries or habitat, recreation or boating, industry, and general or unspecified; Table B). Requirements were also grouped into flow type categories (e.g., minimum flow rate, maximum flow rate, ramping rate). Additional information related to flow requirements such as the augmentation time-period and whether the flow rate was continuous (i.e., condition must be present at all-times) or instantaneous (i.e., condition present at a point in time) was also extracted from the licenses. Some licenses had specific flow requirements based on whether the project was in a wet, dry, or normal water year. If that information was presented in the license, it was also included in the data set. The location within the project was noted, hereafter, zone, in the dataset for flow requirements relating to specific areas of hydropower projects (Dam, Powerhouse, Bypass Reach). Maximum discharge capacities of hydropower facilities were also extracted from both the Existing Hydropower Assets (EHA) data set and the National Inventory of Dams (NID) databases. Each facility was coded with project identification codes from the EHA dataset to facilitate cross-referencing between datasets.

13 HYDRO ENERGY↗
NASA NTRS2002

Understanding Fluid Shifts in the Brain: Choroidal Regulation Involved in the Cerebral Fluid Response to Altered Gravity

Fluid balance and regulation of body fluid production are critical aspects of life and survival on Earth. In space, without gravity exerting its usual downward pulling effect, the fluids of the human body shift in an unnatural, headward direction. After awhile, humans and other mammalian species adapt to the microgravity environment which leads to changes in the regulation and distribution of these body fluids. Previous spaceflight experiments have indicated that production of fluid in the brain and spinal cord, cerebrospinal fluid (CSF), might be reduced in rats exposed to microgravity. In this experiment conducted by Dr. Jacqueline Gabrion (University of Pierre and Marie Curie, France), proteins important for CSF production, and several molecules that regulate water and mineral transport, will be investigated in rats flown on the Shuttle. Dr. Gabrion and her team will determine the amounts of these proteins and molecules present in the brain in order to evaluate whether any changes have taken place during the rats' adaptation to microgravity. The levels of different aquaporins (proteins that act as a channel for water transport in and out of cells) will also be investigated in other areas of the brain and body to better understand the regulatory responses affecting these important water channel proteins. In addition to producing essential and basic information about fluid production in the brain and body, this experiment will reveal fundamental information about the mechanisms involved in cerebral adaptation and fluid balance during spaceflight.

Gabrion, Jaqueline↗
DOE OSTI2023

Aqueous Bromide Discharges from U.S. Coal-Fired Power Plants: Points of Origin, Concentration Ranges, and Effluent Treatment Costs

Bromide discharges from coal-fired power plants have received increased attention from regulatory bodies due to their contribution to the formation of disinfection byproducts (DBPs) in downstream drinking water treatment plants. Here, this paper characterizes the relative contributions of bromide from coal feedstocks and bromine-based mercury control processes, estimates the distribution of bromide concentrations at 85 active coal-fired power plants across the United States (U.S.) with wet flue gas desulfurization units, and estimates the cost of bromide removal from wastewater discharge using year 2020 data. Bromide discharges are estimated at the plant level using a combination of the reported coal rank and composition combusted, estimates of bromide addition in mercury control techniques under multiple halogen addition scenarios, and the estimated flue gas desulfurization (FGD) wastewater flow rate. The median, simulated plant-level estimation of total FGD wastewater flow is 18.3 gallons/min at a bromide concentration of 319 mg/L, equivalent to ~11.6 tonnes/year of bromide discharges to the environment. Next, we evaluated the expected cost of employing the best available technology (BAT) to control bromide discharges in FGD wastewater to prevent contributions to DBP formation. Treatment would need to remove more than 99.8% of bromide to reach the 0.2 mg/L voluntary incentive program (VIP) limit. The total cost of treatment depends on whether disposal is on- or off-site; the average costs for all plants combined come to an average of $110 million ($95.2/kgal) in 2021 U.S. dollars for on-site disposal, or $134 million ($115/kgal) for off-site disposal.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2020

AniMACCS User Guide

AniMACCS is a utility code in the MELCOR Accident Consequence Code System (MACCS) software suite that allows for certain MACCS output information to be visually displayed and overlaid onto a geospatial map background. AniMACCS was developed by Sandia National Laboratories for the U.S. Nuclear Regulatory Commission. MACCS is designed to calculate health and economic consequences following a release of radioactive material in the atmosphere. MACCS accomplishes this by modeling the atmospheric dispersion, deposition, and consequences of the release, which depend on several factors including the source term, weather, population, economic, and land-use characteristics of the impacted geographical area. From these inputs, MACCS determines the characteristics of the plume, as well as ground and air concentrations as a function of time and radionuclide.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2023

BISON Fuel Fragmentation Relocation and Dispersal (FFRD) Assessment Database for Eventual Use in Bayesian Calibration

Existing light-water reactor (LWR) fuel vendors have been interested in seeking increased discharge burnups of nuclear fuel rods for improved economics for quite a few years. With increased burnups come additional challenges that must be addressed. It has been experimentally observed that average burnups higher than the current regulatory limit of 62 MWd/kgU may undergo fuel fragmentation, relocation, and dispersal (FFRD) during a loss-of-coolant accident (LOCA). Industry must demonstrate approaches to mitigate FFRD. In an effort to support industry, the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program within the U.S. Department of Energy (DOE) has for several years invested in developing multiscale models and creating a validation/assessment database for these models to study the mechanisms driving FFRD. This report provides an update on changes made to the assessment database and new models added to BISON to support the study of fuel rod behavior during FFRD. An effort has been initiated this year to begin adding dedicated inputs to the publicly available Virtual Test Bed (VTB) repository for industry use. A section of this report details the efforts made in this area. NEAMS has recently developed new capabilities in the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework’s stochastic tools module for calibration using Bayesian inference. The goal in the future is to use these capabilities to calibrate and identify weaknesses in the existing BISON models for FFRD. The report concludes with a discussion on the models most likely to benefit the most from such calibration.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Enabling Renewable Energy While Protecting Wildlife: An Ecological Risk-Based Approach to Wind Energy Development Using Ecosystem-Based Management Values

Acceptance of wind energy development is challenged by stakeholders’ concerns about potential effects on the environment, specifically on wildlife, such as birds, bats, and (for offshore wind) marine animals, and the habitats that support them. Communities near wind energy developments are also concerned with social and economic impacts, as well as impacts on aesthetics, historical sites, and recreation and tourism. Lack of a systematic, widely accepted, and balanced approach for measuring the potential damage to wildlife, habitats, and communities continues to leave wind developers, regulators, and other stakeholders in an uncertain position. This paper explores ecological risk-based management (RBM) in wind energy development for land-based and offshore wind installations. This paper provides a framework for the adaptation of ecosystem-based management to wind energy development and examines that framework through a series of case studies and best management practices for applying risk-based principles to wind energy. Ten case studies indicate that wind farm monitoring is often driven by regulatory requirements that may not be underpinned by scientific questions. While each case applies principles of adaptive management, there is room for improvement in applying scientific principles to the data collection and analysis. Challenges and constraints for wind farm development to meet RBM framework criteria include collecting sufficient baseline and monitoring data year-round, engaging stakeholder facilitators, and bringing together large and diverse scientific teams. The RBM framework approach may provide insights for improved siting and consenting/permitting processes for regulators and their advisors, particularly in those nations where wind energy is still in the early development stages on land or at sea.

17 WIND ENERGY↗
DOE OSTI2020

Tracking Radioactive Isotopes in HVAC and Application for Hot Cell Analyses - 20155

In recent years, the surge in the number of isotope production facilities under design has increased the need to analyze isotope migration in facility Heating, Ventilation, and Air Conditioning (HVAC) during normal operations and accident scenarios. These facilities are used to produce isotopes for medical, security, and industrial applications and as such are subject to license and regulatory requirements 10CFR20, 10CFR30, 10CFR50, and 10CFR70. GOTHIC, a general-purpose thermal-hydraulics software package, includes the ability to model isotopic tracers, radioactive decay and isotope migration as well as HEPA and charcoal filters for isotope retention. A GOTHIC model was developed by Zachry Nuclear Engineering (ZNE) to examine the effect of negative room pressure, HEPA filtration, and HVAC fluctuations on radiation areas, hot cells and gloveboxes. Radioactive tracers were used to simulate the concentration of spills within contaminated areas, track the migration of isotopes of interest, and determine the isotopic retention and buildup on facility HEPA filters. A variety of isotopes with concern to dose (e.g., Kr-85, Sr-90, I-131, etc.), including their decay and progeny, are included in the analysis. Negative pressures are maintained in the regions of interest by a representative central HVAC system equipped with a volumetric fan that exhausts to the environment after a series of isolation valves and HEPA filters. GOTHIC is an industry trusted tool for providing engineering solutions for a variety of applications, including fission product tracking, aerosol and particulate transport and ventilation assessments. The software provides an integrated analysis environment that includes a graphical user interface (GUI) for constructing analysis models, a numerical solver that includes parallel processing capabilities and a post-processor for evaluating simulation results. It solves the conservation equations for mass, momentum and energy for multicomponent, multi-phase flow in lumped parameter and multi-dimensional geometries (1, 2, or full 3D), including the effects of turbulence, diffusion and buoyancy. It has been developed and maintained under a Quality Assurance program in compliance with the requirements of 10CFR50 Appendix B and applicable portions of ASME NQA-1 since 1995. GOTHIC has been used for assessing both forced and natural convection conditions for a wide range of applications, including: - Tracking concentration of hazardous gases and chemicals for habitability and safety assessments - Determining ventilation and filtration requirements and optimizing location and arrangement of these systems - Room heat-up, including diverse and Flexible coping strategies for Extended Loss of AC Power (FLEX/ELAP) - Equipment Qualification (EQ) A distinctive feature of GOTHIC is the ability to track many different fields/substances in a simulation, including user defined tracer elements, in the liquid, vapor and droplet fields as well as surfaces and filters. This capability allows GOTHIC to model fission product transport and release or the removal of particulates or harmful toxins from exhaust gases using a spray scrubber or other types of filtration systems. GOTHIC also includes models for engineered equipment, such as fans, filters, charcoal filters, dryers/demisters, dampers, etc. The aerosols and other filtered material are removed or accumulated in these components. The range of aerosol and radiological applications that GOTHIC has been used for includes: - Source Term: Primary Coolant (Equilibrium) Activity; Non-Water Coolant Source/Leakage. - Conditions for Iodine Re-evolution: Sump/Suppression Pool Conditions and pH; - RWST Conditions and pH. - Isotope Removal Mechanisms: Containment Sprayed and Unsprayed Region Mixing; Charcoal Filter Heating due to Iodine decay. - Radionuclide Transport and Decay: Post-LOCA Release in containment; Transport between connected Compartments and vent systems; Groundwater transport of radionuclides. - Non-Newtonian Fluid modeling for sludge, waste tanks, etc. ADAMS ML071581053 (titled 'Best Practice Guidelines for the use of CFD in Nuclear Reactor Safety Applications') poses guidelines for applying single phase CFD codes in nuclear reactor safety problems and GOTHIC is listed as a 'tool for 3D flows' and 'dispersal and deposition of radionuclides.' The Nuclear Quality Assurance (NQA) pedigree of GOTHIC is an important aspect for applications in the nuclear industry. The fundamental tracer models (convective transport, molecular and turbulent diffusion, removal mechanisms, etc.) have been verified using analytical solutions and validated against applicable separate effects tests. Also, GOTHIC has been benchmarked to many integrated effects tests, including Phebus FP (Fission Product). GOTHIC gives good agreement for the buildup and decay of fission products in Phebus Test 3. The model developed by ZNE demonstrates GOTHIC's applicability and acceptability for use in analyzing the migration and retention of radioactive isotopes and their progeny in normal operation and accident scenario analyses for isotope production facilities, hot cells, and gloveboxes. The tracer activities calculated by GOTHIC can then be used in downstream radiation transport and shielding codes like RADTRAD-NAI{sup C}, MCNP{sup R}, and MicroShield{sup R} to determine on-site and of-site doses. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Device for steam cladding oxidation testing at TREAT

To compare the chemical degradation of conventional zirconium alloy (Zry) cladding to advance silicon carbide (SiC) cladding in a post loss of coolant accident (LOCA) environment, new nuclear testing capabilities are necessary. The Transient Reactor Test (TREAT) Facility at Idaho National Laboratory (INL) has matured its transient fuel testing capabilities since its 2017 restart. The most recent experiment architecture is the Transient Water Irradiation System in TREAT (TWIST), which is designed to support qualification of accident tolerant fuels in light water reactors. INL has designed and analyzed a natural circulation steam flow modification for TWIST to produce prototypic conditions of cladding oxidation. The in-situ device will be electrically heated to drive natural circulation. Moreover, the SiC cladding requires heating above 1700 °C to observe failure, thus internal prototypic nuclear heating with radiation effects will be used. Thermal hydraulic analysis with RELAP5-3D (Reactor Excursion and Leak Analysis Program) estimated steam fluxes greater than 50 mg cm −2 s −1 can be achieved. These fluxes are adequate to test Zry cladding according to draft regulatory guides and to test SiC cladding according to past experiments.

Oxidation↗
DOE OSTI2024

Regulatory Spike Testing of RPP-WTP LAW and HLW Glasses for Compliance with Land Disposal Restrictions, VSL-03R3760-1, Rev. 1

The United States Department of Energy’s (DOE’s) Hanford site is the current location of storage of about 50 million gallons of mixed waste. This waste is stored in underground tanks at the Hanford site and is both a listed and characteristic waste, as defined in 40 CFR Part 261, and a dangerous waste according to Chapter 173-303 of the Washington Administrative Code (WAC). The waste is also subject to the Land Disposal Restrictions (LDR) (40 CFR Part 268 and WAC 173-303-140). The River Protection Project - Waste Treatment Plant (RPP-WTP) will provide DOE with a means for treating this waste by vitrification (for subsequent disposal). The tank waste will be partitioned into low and high activity fractions, which will then be vitrified respectively into Immobilized Low Activity Waste (ILAW) and Immobilized High Level Waste (IHLW) products. The ILAW product will be disposed of in an engineered facility on the Hanford site while the IHLW product will be directed to the national deep geological disposal facility for high level nuclear waste. The ILAW and IHLW products must meet a variety of requirements with respect to protection of the environment.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Business Environment Study (Subtask 5.1)

In 2016, WVR acquired the Wabash Integrated Gasification Combined Cycle (IGCC) Plant north of Terre Haute, Indiana. Initially, WVR intended to use the plant to produce ammonia using syngas converted to hydrogen. Part of the business plan was to capture and sequester the CO 2 byproduct with the goal of a net-zero carbon emitting plant. Now, with the demand for clean hydrogen-based power and fuel cell energy, the plant intends to produce power and sell hydrogen as a fuel source, still with the intent to sequester CO 2 and achieve net-zero emissions. The Wabash CarbonSAFE project’s objectives are to establish the feasibility of developing a commercial-scale geological storage complex at the WVR plant in Vigo County, Indiana, for storage of 50 million tonnes or more of CO 2 . The plant is expected to produce up to 2 million tons (1.82 million tonnes) of CO 2 annually as a byproduct of hydrogen production. Wabash CarbonSAFE has examined the feasibility of geologic storage of the CO 2 in the Potosi Dolomite Storage Complex of the Illinois Basin via an onsite characterization well at the WVR plant site. This document explores the business requirements to undertake such a project, outlining the outside influences on a business venture such as legislation, legal, regulatory, and business climate factors. This document then discusses the CO 2 source, potential partner sources, and the business financials that allow CCS to be commercially viable for Wabash Valley Resources.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
NASA NTRS2002

Water and Energy Dietary Requirements and Endocrinology of Human Space Flight

Fluid and energy metabolism and related endocrine changes have been studied nearly from the beginning of human space flight in association with short- and long-duration flights. Fluid and electrolyte nutrition status is affected by many factors including the microgravity environment, stress, changes in body composition, diet, exercise habits, sleep cycles, and ambient temperature and humidity conditions. Space flight exposes astronauts to all these factors and consequently poses significant challenges to establishing dietary water, sodium, potassium, and energy recommendations. The purpose of this article is to review the results of ground-based and space flight research studies that have led to current water, electrolyte, and energy dietary requirements for humans during space flight and to give an overview of related endocrinologic changes that have been observed in humans during short- and long-duration space flight.

short duration↗
DOE OSTI2026

Genomic signatures in Variovorax enabling colonization of the Populus endosphere

Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.

comparative genomics↗
DOE OSTI2024

Dynamics of ER stress-induced gene regulation in plants

Endoplasmic reticulum (ER) stress is a potentially lethal condition that is induced by the abnormal accumulation of unfolded or misfolded secretory proteins in the ER. In eukaryotes, ER stress is managed by the unfolded protein response (UPR) through a tightly regulated, yet highly dynamic, reprogramming of gene transcription. Although the core principles of the UPR are similar across eukaryotes, unique features of the plant UPR reflect the adaptability of plants to their ever-changing environments and the need to balance the demands of growth and development with the response to environmental stressors. Here, the past decades have seen notable progress in understanding the mechanisms underlying ER stress sensing and signaling transduction pathways, implicating the UPR in the effects of physiological and induced ER stress on plant growth and crop yield. Facilitated by sequencing technologies and advances in genetic and genomic resources, recent efforts have driven the discovery of transcriptional regulators and elucidated the mechanisms that mediate the dynamic and precise gene regulation in response to ER stress at the systems level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genetic circuit design automation for yeast

Cells can be programmed to monitor and react to their environment using genetic circuits. Design automation software maps a desired circuit function to a DNA sequence, a process that requires units of gene regulation (gates) that are simple to connect and behave predictably. This poses a challenge for eukaryotes due to their complex mechanisms of transcription and translation. To this end, we have developed gates for yeast (Saccharomyces cerevisiae) that are connected using RNA polymerase flux as the signal carrier and are insulated from each other and host regulation. They are based on minimal constitutive promoters (~120 base pairs), for which rules are developed to insert operators for DNA-binding proteins. Using this approach, in this work we constructed nine NOT/NOR gates with nearly identical response functions and 400-fold dynamic range. In circuits, they are transcriptionally insulated from each other by placing ribozymes downstream of terminators to block nuclear export of messenger RNAs resulting from RNA polymerase readthrough. Based on these gates, Cello 2.0 was used to build circuits with up to 11 regulatory proteins. A simple dynamic model predicts the circuit response over days. Genetic circuit design automation for eukaryotes simplifies the construction of regulatory networks as part of cellular engineering projects, whether it be to stage processes during bioproduction, serve as environmental sentinels or guide living therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Advanced Reactor Cyber Analysis and Development Environment (ARCADE) for System-Level Design Analysis

Cybersecurity is a persistent concern to the safety and security of Nuclear Power Plants (NPPs), but has lacked data-driven, evidence-based research. Rigorous cybersecurity analysis is critical for the licensing of advanced reactors using a performance-based approach. One tool that enables cybersecurity analysis is modeling and simulation. The nuclear industry makes extensive use of modeling and simulation throughout the decision process but lacks a method to incorporate cybersecurity analysis with existing models. To meet this need, the Advanced Reactor Cyber Analysis and Development Environment (ARCADE) was developed. ARCADE is a suite of publicly available tools that can be used to develop emulations of industrial control system devices and networks and integrate those emulations with physics simulators. This integration of cyber emulations and physics models enables rigorous cyber-physical analysis of cyber-attacks on NPP systems. This report provides an overview of key considerations for using ARCADE with existing physics models and demonstrates ARCADE’s capabilities for cybersecurity analysis. Using a model of the Small Modular Advanced High Temperature Reactor (SmAHTR), ARCADE was able to determine the sensitivity of the primary heat exchangers (PHX) to coordinated cyber-attacks. The analysis determined that while the PHX’s failures cause disruption to the reactor, they did not cause any safety limits to be exceeded because of the plant design, including passive safety features. Further development of ARCADE will enable rigorous, repeatable, and automated cyber-physical analysis of advanced reactor control systems. These efforts will also help reduce regulatory uncertainty by presenting similar types of cybersecurity analyses in a common format, driving standard approaches and reporting.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗