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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Multi-Mechanism Flood Hazard Assessment: Critical Review of Current Practice and Approaches

This report documents the initial findings from the Nuclear Regulatory commission (NRC)-sponsored research project Methods for Estimating Joint Probabilities of Coincident and Correlated Flooding Mechanisms for Nuclear Power Plant Flood Hazard Assessments.1 This research project is a part of NRC’s Probabilistic Flood Hazard Assessment (PFHA) Research Program and will aid the development of guidance on the use of PFHA methods to evaluate infrastructure safety for existing and proposed US nuclear power plants (NPPs). More specifically, this project intends to provide technical background for the development of flood hazard curves for multi-mechanism floods (MMFs). MMFs are flood events caused by more than one flooding mechanism (e.g., flood events due to the simultaneous occurrence of precipitation-induced river flooding and storm surge). Project activities include three main tasks: Task 1—Survey of current concepts and methods in assessing MMF hazards; Task 2—Critical assessment of selected methods and approaches for quantifying probabilistic MMF hazard risk; Task 3—Development of example case studies to illustrate best practices for quantifying probabilistic MMF hazard risk The initial findings from Tasks 1 and 2 are documented in this report. Task 1 comprised a survey of approaches and methods that have been applied to understand and assess flood hazards due to MMFs. Task 2 involved a critical review of the selected approaches and methods. To that end, the scope of this report includes documentation of (1) a reconnaissance-level survey of the current state of concepts and practice for MMF hazard assessment; (2) a generalized MMF assessment framework to address the distinctions among various types of flood-forcing phenomena, flood mechanisms (grouped into three mechanism types), and flood severity metrics; (3) a wide-ranging survey of approaches and methods that have been applied to various flooding phenomena and settings; and (4) a critical assessment of MMF hazard assessment methods. Studies were identified involving MMFs related to coastal flooding mechanisms, fluvial (rivers/streams) flooding mechanisms, and associated combinations of coastal and fluvial flooding mechanisms. Studies were also identified that address MMFs involving coastal and fluvial flooding mechanisms as well as coastal flooding mechanisms along with extreme precipitation (without specific attribution to fluvial or pluvial mechanisms). The studies identified for review in this report included assessments at varying spatial scales (from local to global) with differing geographic regions of focus using both observed and synthetic data. The majority of studies identified and reviewed were site-specific assessments focusing on relatively short return periods. Studies considered a range of flood severity metrics, made differing assumptions regarding the occurrence of extrema, and used multiple statistical techniques; the use of copulas for the development of joint distributions was a particularly popular analysis technique. The literature review highlighted the differences among existing studies relative to terminology used, means of presenting results, framework and techniques employed, and level of sophistication regarding the number and types of variables considered. Despite the significant diversity in existing studies, the review identified several promising techniques that will be considered in future work under this project, including the development of joint distributions for MMFs using copula and Bayesian-motivated approaches.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2021

Industry Level Integrated Fire Modeling Using Fire Risk Investigation in 3D (FRI3D)

The software Fire Risk Investigation in 3D (FRI3D) has been developed over the last 2 years to integrate 3D spatial modeling with existing fire probabilistic risk assessment (PRA) models and fire simulation codes. The goal of this research and development is to automate many of the fire analysis manual tasks to reduce industry efforts in the initial fire modeling and operational costs for the model maintenance and evaluations required during normal plant operations. The tasks for Fiscal Year (FY) 2021 include first testing the FRI3D modeling capabilities by importing an industry fire model into FRI3D and making a 3D model of a complex/high-risk significant area. (For this work, the switchgear room was chosen.) Then, the second task of FY 2021 is to develop a dynamic fire PRA process that can help optimize traditional fire PRA models. The switchgear room model will be used for the dynamic fire PRA work. This report describes the work and insights learned when using FRI3D software to model both a Nuclear Regulatory Report (NUREG) example models and a full industry switchgear room.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Complementing the CCS Class VI Well Permit Process with DOE-NETL's SMART Initiative Tools and Workflows

This is a presentation on model explorer developed under SMART initiative Task 2. Our team will present the current progress of the model explorer in using machine learning models to accelerate CCS project at GWPC meeting. Model explorer bring new capabilities, (fast, Realtime, and accurate) that can help CCS stakeholders including regulatory agencies, public and site operators make faster decisions and process information and data.

Hosseini, Seyyed↗
DOE OSTI2025

Transition of SRT Source Term Software to Modern Version Control System to Enable More Efficient Verification, Validation, and User Engagement

The Simplified Radionuclide Transport (SRT) code assists in reactor design and licensing by providing a detailed analysis of radionuclide transport under specific transient scenarios. This analysis is essential for ensuring that reactors meet safety and regulatory standards before they are authorized to operate. Mechanistic source term analysis, which involves a realistic evaluation of radionuclide behavior from the source to the environment, is a key component of this process. It provides a comprehensive understanding of potential release scenarios, supporting the development of robust safety measures.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Building Nuclear-Specific Cybersecurity Expertise in Higher Education

The rapid digitalization of nuclear power plants (NPPs) and the deployment of advanced and small modular reactors (A/SMRs) have expanded the cybersecurity attack surface within the nuclear sector. This evolution introduces unique challenges beyond those faced in general information technology (IT), operational technology (OT) and industrial control system (ICS) security, due to nuclear power’s regulatory rigor, safety-critical nature, and operational needs. A pressing workforce gap persists; cybersecurity graduates typically lack nuclear-specific context and retraining them for industry readiness requires 12–18 months, creating a significant burden. This paper addresses this gap by defining the domains of knowledge that nuclear cybersecurity specialists must master, spanning cybersecurity, nuclear engineering, OT/ICS security, and regulatory governance. We propose a curricular framework integrating technical, regulatory, and applied learning components to accelerate workforce readiness. Our approach builds on existing findings that current curricula inadequately integrate nuclear engineering and cybersecurity, shifting the discourse from why specialization is needed to what knowledge must be taught. The recommendations have implications for workforce development and long-term resilience of the nuclear energy sector.

99 - GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

Considerations for Regulation and Practical Implementation of Analyses of Inadvertent Human Intrusion - 20169

Recommendations from the International Commission for Radiological Protection (ICRP) and the International Atomic Energy Agency (IAEA) identify the need to consider potential inadvertent human intrusion into a near-surface radioactive waste disposal facility when developing limits for radionuclide concentrations that can be disposed. The recommendations also provide perspective on expectations for performance criteria and general assumptions for such analyses. Inadvertent human intrusion analyses are conducted to address the potential failure of institutional controls and loss of memory of a disposal facility. The analyses consider potential consequences of human actions that result in unknowingly bringing waste to the surface. Inadvertent human intrusion scenarios consider potential impacts to someone involved in an activity that actually disturbs the waste (e.g., drilling or excavation of a basement) or that exposes the person to emanations from the waste (e.g., radioactive gases) and also for the case where there may be longer term exposures to waste that has been brought to the surface. In practice, inadvertent human intrusion analyses have proven to be a critical consideration for the development of waste classification systems and for the determination of disposal requirements and limitations on wastes that can be disposed at shallow depths. The IAEA implemented a project on Human Intrusion in the context of Disposal of Radioactive waste (HIDRA) to further explore the regulatory expectations and practical implementation of analyses of potential inadvertent human intrusion. The paper begins with a discussion of international recommendations related to consideration of inadvertent human intrusion and then summarizes examples of some topical considerations related to addressing inadvertent human intrusion that are being discussed as part of the second phase of the HIDRA project. The topical considerations are planned to be addressed in a formal IAEA publication. All information in this paper simply reflects on-going project discussions and no formal recommendations are implied for these topical considerations at this time. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Multifaceted Challenges and Opportunities Associated with Small Modular Reactors in Africa: A Nonproliferation Perspective

In response to the increasing global energy demands driven by industrialization and the urgent need for decarbonization, this study explores the potential of Small Modular Reactors (SMRs) as a sustainable energy solution in Africa. With a focus on nonproliferation concerns, the paper assesses Africa's energy landscape, emphasizing the need for diverse and reliable power sources. While highlighting the scalability and cost-effectiveness of SMRs, the analysis acknowledges potential challenges associated with adhering to the Nonproliferation Treaty with their mass deployment in the African continent. Examining regulatory frameworks, international cooperation, and security protocols, the study also underscores the importance of regional collaboration to prevent the misuse of nuclear technology for military and malicious purposes. The economic and geopolitical implications of SMR deployment in Africa are also investigated, considering its contributions to energy security and economic growth. Drawing insights from successful case studies, the paper concludes by synthesizing key findings and proposing recommendations for policymakers and stakeholders. These recommendations encompass regulatory enhancement, capacity building, technology transfer, and diplomatic efforts to strengthen nuclear security, nonproliferation, and safeguards. The overarching aim is to advocate for a balanced approach that maximizes the benefits of SMRs while mitigating associated risks to ultimately contribute to the sustainable and secure development of nuclear energy in Africa.

Prah, Christina↗
DOE OSTI2024

1. Physical Security Engineering by Design for Nuclear Facilities; 2. Nuclear Power Plant Site Security Management – A Security Strategy; 3. The UAE Women in Nuclear Energy Security

1. Security by design, or SeBD, is a comprehensive approach that integrates the physical protection system of a nuclear plant into every stage of its existence. This includes planning, designing, constructing, commissioning, and operating the facility, using a combination of analytical, physical, technological, and procedural measures. Essentially, SeBD involves intentionally applying and incorporating security into all aspects of design and operation throughout the entire lifecycle of a facility. By implementing this methodology throughout various phases such as program development, process implementation, staff training and procedures management in conjunction with plant equipment, facilities can be optimized to minimize security risks without compromising functional design requirements. This ultimately improves the overall security posture of the site and reduces the need for costly modifications or additional security resources post-design. 2. A site security strategy is a living document that is revised on a periodic or event-driven basis, ensuring that site security operations and corresponding procedures provide long-term, effective protection for the entire nuclear power plant (NPP) site. A site security strategy aims to mitigate threats across the entire NPP site via in-depth defense approaches and mutual support; therefore, if a layer is omitted or altered, then the effect across all layers must be re-evaluated. Therefore, the aim of the site security strategy is to provide an appropriate, scalable security regime that deters, denies, delays, and detects incidents and, equally importantly, reassures legitimate users and the regulator that due diligence and regulatory compliance have been achieved, ensuring that the site is safe and secure. Robust access control for vehicles and pedestrians is at the heart of the strategy. Vehicle and pedestrian searching and screening are seen as the strongest mitigation methods against vehicle- and pedestrian-borne attacks. The security strategy must also be supported through comprehensive staff training and the development of robust processes, procedures, and planning. If all these measures are to be effective, then training must be implemented during each phase of construction, partial operation/commissioning, and full operation. No single element of site security is completely isolated from the influence of other elements. Ideally, consideration of all key elements will result in a security strategy that is integrated and proportional to the threat and that does not over specify individual security solutions through the application of isolated measures but rather applies a holistic, all-encompassing approach. 3. When women enter the labor force, numerous positive outcomes emerge, including increased GDP, educational gains, and decreased maternal mortality. Despite these benefits, women's employment rates and equality vary significantly worldwide as does support for women in the workforce. This paper will explore the multifaceted benefits of women's employment, the factors influencing labor force participation rates, and the urgency to achieve gender equality as outlined in the 2015 United Nations Sustainable Development Goals (SDGs). It will then examine the emerging presence of women in the traditionally male-dominated nuclear field, specifically within the United Arab Emirates (UAE) as a testament to their resilience and determination to break social norms and advance gender equality.

Zineddin, Dr. Z.↗
DOE OSTI2021

CATMoS: Collaborative Acute Toxicity Modeling Suite

Background: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. Objectives: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different endpoints: LD50 value, U.S. Environmental Protection Agency hazard categories, Globally Harmonized System for Classification and Labelling hazard categories, very toxic chemicals (LD50 =50 mg/kg), and non-toxic chemicals (LD50 >2000 mg/kg). Methods: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. Results: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared to in vivo results. Discussion: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for over 800,000 chemicals have been made available via the NTP’s Integrated Chemical Environment. The models are also implemented in a free, standalone open-source tool, OPERA, which allows predictions of new and untested chemicals to be made.

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

Recent Developments in Deployment of CCS Projects in the Offshore Gulf of Mexico

In the last year, since the passage of the IRA, there have been over 100 new CCUS project announcements in the U.S. This presentation provides an overview of the recent Offshore Gulf of Mexico (GoM) CCS project announcements attributable to 45Q and improvements in project economics. It also examines how the remaining regulatory hurdles to potentially broader CCUS deployment in the Offshore GoM, are being addressed.

Zaremsky, Connie↗
DOE OSTI2020

Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection

Neisseria gonorrhoeae is a Gram-negative diplococcus that is responsible for the sexually transmitted infection gonorrhea, a high-morbidity disease in the United States and worldwide. Over the past several years, N. gonorrhoeae strains resistant to antibiotics used to treat this infection have begun to emerge across the globe. Thus, new treatment strategies are needed to combat this organism. Here, we utilized N. gonorrhoeae transcriptomic data sets, including those obtained from natural infection of the human genital tract, to infer the first global gene coexpression network of this pathogen. Interrogation of this network revealed genes central to the network that are likely critical for gonococcal growth, metabolism, and virulence, including genes encoding hypothetical proteins expressed during mucosal infection. In addition, network analysis revealed overlap in the response of N. gonorrhoeae to incubation with neutrophils and exposure to hydrogen peroxide stress in vitro. Network analysis also identified new targets of the gonococcal global regulatory protein Fur, while examination of the network neighborhood of genes allowed us to assign additional putative categories to several proteins. Collectively, the characterization of the first gene coexpression network for N. gonorrhoeae described here has revealed new regulatory pathways and new categories for proteins and has shown how processes important to gonococcal infection in both men and women are linked. This information fills a critical gap in our understanding of virulence strategies of this obligate human pathogen and will aid in the development of new treatment strategies for gonorrhea.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2021

Proceedings from the State of the Science and Technology for Minimizing Impacts to Bats from Wind Energy

The U.S. Department of Energy Wind Energy Technologies Office (DOE WETO), and the National Renewable Energy Laboratory convened a workshop entitled the State of the Science and Technology for Minimizing Impacts to Bats from Wind Energy on 13–14 November 2019. The objectives of the workshop were to (1) Identify the current impact minimization measures that are, or can be, used to reduce bat fatalities at wind energy facilities, (2) Assess the current effectiveness of those minimization measures, (3) Identify and assess the research and development (R&D) opportunities needed to optimize and improve the effectiveness of current minimization and deterrent technologies and inform the development of future solutions; and (4) Identify potential emerging or novel methods for informing impact minimization measures at or around wind energy facilities. Specifically, the workshop focused on deterrent and curtailment strategies. For deterrents, the discussion centered on the existing technology (i.e., ultrasonic deterrents, dim-UV light, and texture coating), integration with wind turbines (either retrofitting or out of the box installation), effectiveness, validation studies, and cost (e.g., technology, installation, validation, and maintenance). For curtailment, the conversation was divided into blanket curtailment (i.e., based on time and wind speed) and smart curtailment (i.e., blanket curtailment plus additional variables such as temperature or bat activity). The workshop included plenary presentations, panels, and breakout sessions to share data and stakeholder perspectives, and engage participants. Although there are several priority topics related to bat and wind energy, this workshop focused the discussion on the current technologies and strategies that are, or can be, used to reduce bat fatalities at wind energy facilities, status of research and development (R&D) of minimization measures, opportunities to optimize costs and improve effectiveness, and potential emerging or novel approaches to explore. This workshop took a holistic approach and discussed all aspects associated with advancing deterrent technologies and curtailment strategies, including the technological, biological, economic, and regulatory barriers faced by the wind energy and wildlife community.

13 HYDRO ENERGY↗
DOE OSTI2021

A Survey of Federal and State-Level Solar System Decommissioning Policies in the United States

In the United States, cumulative installed utility-scale solar photovoltaic (PV) capacity reached more than 60 gigawatts (GW)dc at the end of 2020 (Davis et al. 2021b). Federal and state renewable energy and net-zero emissions policies will continue to drive solar development in the United States with installed utility-scale PV projected to quadruple (240 GWdc) by 2030 (Davis et al. 2021a; Heeter 2014). Although more than 75% of all U.S. installed utility-scale PV came online in the last 5 years, federal, state, and local governments are planning for system decommissioning (Davis et al. 2021b). Our research found that as of April 2021, one federal agency, the Bureau of Land Management (BLM), and 15 U.S. states have solar decommissioning policies in place. North Carolina is also in the process of drafting solar decommissioning regulations, and at least 4 states (Maine, Pennsylvania, West Virginia, Texas) proposed solar decommissioning bills in the 2021 legislative session. This report provides a survey and brief overview of both federal and U.S. statewide solar decommissioning policies, and a discussion of some of the potential impacts different policy designs may have on utility-scale solar development, including impacts that might influence construction timelines and over project costs.

14 SOLAR ENERGY↗
DOE OSTI2026

Human Factors Considerations for Hydrogen Rail Refueling and Maintenance

The Federal Railroad Administration (FRA) contracted Sandia National Laboratories to review the risks introduced specifically through human interactions within hydrogen rail refueling and maintenance activities and present recommendations for future system development and implementation. Due to the lack of domestic hydrogen-powered trains at the time of review, observational data was collected on analogous existing systems to consider various ways hydrogen might be implemented within future designs. The team developed 50 human factors design guidelines through analysis of human risk factors. Because hydrogen rail systems are still in the early design stage, the resulting human factors guidelines represent general best practices and do not include specific design features. The research team recommends design and regulatory agencies include a Human Factors Engineer in the design and review process to ensure the guidelines are appropriately implemented and verified.

08 HYDROGEN↗
NASA NTRS2001

Consequences of contamination of the spacecraft environment: immunologic consequences

Long-term space voyages pose numerous known and unknown health hazards, to the human immune system. Well-studied clinical examples of secondary immunodeficiencies created on Earth, lead one to predict that the conditions of prolonged space flight would weaken the human immune responses that normally hold infection and cancer in check. From evidence gathered from humans flown for prolonged periods in space and from human models of space flight studied on Earth it is reasonable to suspect that space travelers to the planet Mars would experience a weakening of immunity. Subtle defects of immune cell structure and function have been observed in astronauts, such as weakening of specific T-lymphocyte recall of specific antigens. Ground-based models also have demonstrated alterations of immune function, such as the elevation of neuroendocrine immune system messengers, interleukin-6, and soluble tumor necrosis factor-alpha receptor in sleep deprivation. Since severe immune compromise the clinical consequences of reactivation of latent virus infections and the development of cancer, has yet to be seen in space flight or in the Earth models, it is extremely important to begin to quantify early changes in immunity to predict the development of immune system collapse with poor clinical outcomes. This approach is designed to validate a number of surrogate markers that will predict trouble ahead. Inherent in this research is the development of countermeasures to reduce the risks of infection and cancer in the first humans going to Mars.

Non-NASA Center↗
DOE OSTI2020

Stochastic Analysis for Long Term Capital Structures, Systems, and Components Refurbishment and Replacement

As commercial Nuclear Power Plants (NPPs) pursue extended plant operation in the form of Second License Renewal (SLR), opportunities exist for these plants to provide capital investments to ensure long-term safe and economic performance. At the current time, several utilities have announced an intention to pursue extended operation for one or more of their NPPs via SLR . The goal of this research is to develop a risk-informed approach to evaluate and prioritize plant capital investments made in preparation for, and during the period of, extended plant operations to support decisions for NPP operations. Since the capital investments are influenced by various factors, such as markets, safety and regulatory, the decision-making process of NPP operations should take into account relevant factors for balancing risks, costs and profits. The traditional method of capital budgeting is based on the priority list of candidate projects using economic measures such as benefit-investment ratio, net present value (NPV) and internal rate of return. In the literatures, the problem of capital budgeting or the variant can be represented by an appropriate knapsack problem. The knapsack approach to capital budgeting takes as input as investment, along with the cost and profit of each project. The objective of capital budgeting is to find the combination of the binary decisions for every investment such that the overall profit is as large as possible. The output is a collection of projects to be carried out, and we refer this selected collection of projects as a project portfolio. One limitation of traditional optimization models for capital budgeting is that they do not account for risk/uncertainty in profit and cost streams associated with individual projects, they do not account for risk in resource availability in future years [1,2,3]. Projects can incur cost over-runs, especially when projects are large, performed infrequently, and when there is risk regarding technical viability, external contractors, and/or suppliers of requisite parts and materials. Occasionally, projects are performed ahead of schedule and with cost savings. Planned budgets for capital improvements can be cut and key personnel may be lost. Or, there may be surprise windfalls in budgets for maintenance activities due to decreased costs for “unplanned” maintenance. In these cases, how should we resolve capital budgeting when we have risk forecasts for costs, profits and budgets? One approach we proposed in this summary is to re-solve the optimization models based on assumed statistical distributions of given parameters. If these distributions were not available, a two-stage stochastic optimization approach can be used to provide priority lists to decision-makers to support better risk-informed decisions [4, 5]. In this summary, we will only focus on the first approach.

42 ENGINEERING↗
DOE OSTI2021

SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning

SMAD4 regulates gene expression in response to BMP and TGFβ signal transduction, and is required for diverse morphogenetic processes, but its target genes have remained largely elusive. Here, we identify the SMAD4 target genes in mouse limb buds using an epitope-tagged Smad4 allele for ChIP-seq analysis in combination with transcription profiling. This analysis shows that SMAD4 predominantly mediates BMP signal transduction during early limb bud development. Unexpectedly, the expression of cholesterol biosynthesis enzymes is precociously downregulated and intracellular cholesterol levels are reduced in Smad4-deficient limb bud mesenchymal progenitors. Most importantly, our analysis reveals a predominant function of SMAD4 in upregulating target genes in the anterior limb bud mesenchyme. Analysis of differentially expressed genes shared between Smad4- and Shh-deficient limb buds corroborates this function of SMAD4 and also reveals the repressive effect of SMAD4 on posterior genes that are upregulated in response to SHH signaling. This analysis uncovers opposing trans-regulatory inputs from SHH- and SMAD4-mediated BMP signal transduction on anterior and posterior gene expression during the digit patterning and outgrowth in early limb buds.

59 BASIC BIOLOGICAL SCIENCES↗