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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Abstract Background Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. Results We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10 −3 ), and combined dataset (p = 1.1 × 10 −4 ). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10 −35 , loss-of-function p = 2.26 × 10 −13 ) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10 −6 , OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. Conclusions In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Electrification of Aircraft: Challenges, Barriers, and Potential Impacts

Small-scale aircraft are being electrified with small e-aircraft already certified to fly and with test flights underway for retrofits of existing aircraft focused on near-term deployment. Internationally, from 2018 to 2020, the number of electric aircraft projects underway increased 50%. These technologies are projected to increase operational efficiency and reduce emissions and noise from a growing aviation sector. This emerging interest in aviation electrification includes aircraft, energy supply equipment, and battery storage manufacturers. Federal agencies are currently funding a variety of efforts including technology research as well as forecasting demand and environmental impacts and state governments have also begun pushing for further investigation in this area. This paper provides an overview of the current state and potential future development of aviation electrification. To understand the types of research questions around current and future challenges for this emerging sector, we consider a case study of the potential deployment of small commercial electric aircraft for existing, under-served markets and consider operational requirements and technical challenges as well as the range of questions that will need to be addressed around charging infrastructure, grid integration, policy and regulatory requirements, and emissions impacts. This case study also outlines potential nearer-term solutions and research areas of interest that will need to be addressed in the longer term at much larger scales and highlights NREL capabilities for addressing these challenges.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Basin-Scale Relicensing Opportunity Product User Guide

The Basin-Scale Relicensing Opportunity products provide a platform for identifying favorable areas for basin-wide collaboration using metrics derived from anticipated Federal Energy Regulatory Commission (FERC) relicensing dates. The hydropower relicensing process requires long-term resource allocation by agencies, hydropower owner/operators, non-governmental organizations, and tribal, state, and federal governments. Basin-scale hydropower relicensing has begun to receive attention as a potential solution for reducing licensing timelines, costs, and uncertainty which can provide benefits to a broad spectrum of participants in the licensing process. Two products were developed: (1) an interactive web map that allows users to browse facilities and rivers of interest and uncover locations for potential collaboration based on FERC relicensing metrics summarized along river reaches and (2) a spreadsheet that contains 1,261 facilities with associated FERC relicensing metrics and that allows users to join these data to others and develop and conduct their own analyses.

13 HYDRO ENERGY↗
DOE OSTI2024

AFC Metallic Fuel Research and Development 5-Year Plan

The mission of the U.S. Department of Energy (DOE) Advanced Fuel Campaign (AFC) program is conducting R&D on nuclear fuel technology that enables near- and long-term implementation of the reactor systems necessary to meet national nuclear energy objectives. Its primary goals align with goals of the DOE Office of Nuclear Energy in sustaining the current LWR fleet through Accident Tolerant Fuels program and Enabling Advanced Reactors. The latter goal is to be achieved through the following subgoals in order of logistical priority: • Establish the qualification basis for reference metallic fuel designs for sodium-cooled fast reactors. • Develop next generation metallic fuel fabrication and design for improved fissile utilization and management. • Develop accelerated fuel development and qualification methodologies. • Identify next generation fuel technologies. The purpose of this document is to serve as a five-year research and development (R&D) plan to achieve the goals identified to support enabling advanced reactor deployment related to metallic fuels starting in 2025. The specific objectives of this document are to: • align program R&D work across technical areas, national laboratories, and with stakeholder interests, and • aid yearly and outyear scope and budgetary planning activities. This plan lays the foundation of databases, capabilities, expertise, and research-commercial-regulatory integration for launching next-generation initiatives in advanced fuel technologies (fuel and cladding) and improved methodologies for achieving accelerated qualification of next generation fuel technologies.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Smart Inverters, Dumb Risk: Taking Control of IBR Security in the Digital Age

This presentation addresses the security challenges posed by Inverter-Based Resources (IBRs) in the modern energy landscape. The presentation highlights the vulnerabilities and risks associated with IBRs, including the potential for cyber-attacks, the impact of insecure defaults, and the systemic risks posed by supply chain dependencies. Key topics covered include: 1) The increasing digital transformation in energy systems and the associated security risks. 2) Specific vulnerabilities in IBRs, including weak passwords, hardcoded credentials, and insecure web application interfaces. 3) The implications of persistent connectivity and the strategic risks posed by foreign-manufactured components. 4) The role of regulatory frameworks, such as NERC CIP, in addressing these challenges and the limitations of current oversight. 5) Practical solutions for mitigating risks, including secure design practices, vendor risk assessments, and the importance of strong passwords and role-based access control. The presentation underscores the necessity of a comprehensive, system-of-systems approach to securing IBRs, emphasizing the need for collaboration across various stakeholders, including operators, developers, and regulators, to ensure the resilience and security of the energy grid.

24 - POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Developing a Prototype Methodology to Rank CO2-EOR Wells and Assess Their Reuse Potential for Geologic Carbon Storage

This paper presents a prototype methodology to assess the possible transition of Class II carbon dioxide-enhanced oil recovery (CO2-EOR) wells to Class VI wells. The focus is on wellbore construction materials—casing, cement, tubing, and the packer—and includes comprehensive workflows to evaluate these materials, with primary emphasis on compliance with Environmental Protection Agency (EPA) Class VI well construction and conversion guidelines. These workflows systematically assess material properties and performance criteria to ensure regulatory compliance and optimize long-term wellbore integrity and functionality. Utilizing Python scripts and JavaScript Object Notation (JSON) representations, the study automates checks on digitized Texas Railroad Commission (TRRC) data to rank wells based on workflow criteria. By emphasizing critical factors such as casing integrity, cementing techniques, tubing compatibility, and packer selection, the methodology helps well owners and operators prioritize wells for potential reuse as CO2 injection wells. Given limitations in digitized data, manual user verification is required in some sections. Future improvements include integrating non-digitized data through web scraping and machine learning techniques. This research serves as a practical guide for stakeholders, supporting environmental compliance and sustainable well operations.

geologic carbon sequestration↗
DOE OSTI2023

Transcriptome and secretome profiling of sensory neurons reveals sex differences in pathways relevant to insulin sensing and insulin secretion

Sensory neurons in the dorsal root ganglia (DRG) convey somatosensory and metabolic cues to the central nervous system and release substances from stimulated terminal endings in peripheral organs. Sex-biased variations driven by the sex chromosome complement (XX and XY) have been implicated in the sensory–islet crosstalk. However, the molecular underpinnings of these male–female differences are not known. Here, we aim to characterize the molecular repertoire and the secretome profile of the lower thoracic spinal sensory neurons and to identify molecules with sex-biased insulin sensing- and/or insulin secretion-modulating activity that are encoded independently of circulating gonadal sex hormones. We used transcriptomics and proteomics to uncover differentially expressed genes and secreted molecules in lower thoracic T5-12 DRG sensory neurons derived from sexually immature 3-week-old male and female C57BL/6J mice. Comparative transcriptome and proteome analyses revealed differential gene expression and protein secretion in DRG neurons in males and females. Furthermore, the transcriptome analysis identified, among others, higher insulin signaling/sensing capabilities in female DRG neurons; secretome screening uncovered several sex-specific candidate molecules with potential regulatory functions in pancreatic β cells. Together, these data suggest a putative role of sensory interoception of insulin in the DRG–islet crosstalk with implications in sensory feedback loops in the regulation of β-cell activity in a sex-biased manner. Finally, we provide a valuable resource of molecular and secretory targets that can be leveraged for understanding insulin interoception and insulin secretion and inform the development of novel studies/approaches to fathom the role of the sensory–islet axis in the regulation of energy balance in males and females.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Flexible Service Contracting for Risk Management within Integrated Transmission and Distribution Systems

The general objective of our project has been to investigate the ability of Independent Distribution System Operators (IDSOs), functioning as linkage agents for Integrated Transmission and Distribution (ITD) systems, to facilitate the flexible availability and usage of reserve in support of ITD system operations. This general objective is in accordance with Order 2222 of the U.S. Federal Energy Regulatory Commission (FERC), titled “Participation of Distributed Energy Resource Aggregations in Markets Operated by Regional Transmission Organizations and Independent System Operators”. The Final Rule for FERC Order 2222 was issued on September 17, 2020. The primary contribution of our project is that we have formulated an innovative energy management Transactive Energy Design (TES) approach for ITD systems that provides promising support for our project objective. Specifically, we have developed a new type of IDSO-managed TES design for distribution system operations, as well as new types of swing contracts permitting IDSOs to participate in transmission system operations as providers of reserve harnessed from distribution system resources in return for appropriate compensation. Together, these design elements constitute a scalable market-based approach facilitating efficient reserve procurement for ITD system operations from a fuller range of power resources. The efficacy of our approach has been demonstrated by means of detailed conceptual analyses as well as test case simulations. To implement the latter, we have developed the ITD TES Platform V2.0, a computational platform that permits the modeling and software implementation of ITD system operations over time. The Electric Reliability Council of Texas (ERCOT) energy region has been used as the empirical anchor for the development of this platform. Our conceptual and test-case work has been reported in a Wiley/IEEE Press book, two refereed book chapters, and seven refereed journal articles. The key components comprising the ITD TES Platform V2.0 have been released as documented open-source software at online GitHub repositories.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Congestion Management Solutions for Enhanced Distribution System Operations with Aggregated Distribution Grid Resources Providing Grid Services and Market Participation

Microgrids and other aggregations of distribution grid resources (DGRs) are poised to actively participate in electricity markets and provide essential grid services in the coming years. In fact, DGRs already play such a role through behind-the-meter (BTM) demand response programs and small-scale BTM dispatchable generation initiatives. At the same time, the rapid growth of artificial intelligence (AI) and cryptocurrency datacenters imposes significant, often unpredictable, demands on the power distribution system. Aggregated DGRs can serve as flexible resources that help mitigate these pressures by using available transmission and distribution capacity more efficiently, supporting resource adequacy and other reliability services, and providing bridge strategies while long-term transmission infrastructure is being developed. The impacts this activity will have on distribution networks are not fully understood and could present significant challenges for distribution utilities due to capacity constraints and the need for congestion management. Technical issues include reverse power flow, variability and possible degradation of equipment integrity, voltage violations, and customer power quality concerns. These issues will likely intensify as electricity market operators across the United States implement Federal Energy Regulatory Commission Order 2222 over the next few years.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Oak Ridge National Laboratory FY 2023 Site Sustainability Plan With FY 2022 Performance Data

At the close of each fiscal year, the US Department of Energy (DOE) Sustainability Performance Division (SPD) issues guidance documents and technical resource aids/tools necessary for DOE sites and national laboratories to complete sustainability reporting requirements. SPD is part of the DOE Office of Asset Management. As required by DOE Order 436.1, Departmental Sustainability, “each site will develop and commit to an annual Site Sustainability Plan (SSP) that identifies its respective contribution toward meeting the DOE’s sustainability goals.” SPD collects and compiles information reported by each site to develop an agency-wide Sustainability Report and Implementation Plan, which is used to report DOE sustainability progress to the federal government as required by all major federal agencies. DOE launched a formal Sustainability Office and annual SSP process in 2011. Each year, Oak Ridge National Laboratory (ORNL), in concert with the Office of Science (SC), provides the resources essential to fulfill its commitment to deliver a complete and accurate SSP report and quality performance data for entry into the DOE Sustainability Dashboard as managed by SPD. The performance data entered by each DOE site are then combined to disclose the progress of each DOE Program Office and are further combined to show comprehensive progress for the agency. The Office of Asset Management provides assistance to program offices in sustaining their missions, freeing up resources by reducing waste, avoiding excess expenditure on utilities, maximizing productivity, and improving the efficiency of facilities and processes. By focusing on mission needs, programs and associated DOE sites can help the agency meet its sustainability goals, as outlined in federal statutory and regulatory requirements. In FY 2022, the SSP guidance was updated to capture requirements from Executive Order (EO) 14008, Tackling the Climate Crisis at Home and Abroad, the Energy Act of 2020 (EAct 20), actions outlined in DOE’s Climate Adaptation & Resilience Plan and Sustainability Plan, and EO 14057, Catalyzing Clean Energy Industries and Jobs Through Federal Sustainability. Updates in SSP guidance help to minimize and streamline reporting while simultaneously addressing updated federal requirements. Per DOE, each SSP report should provide an overview of the site’s planned actions, as well as an overview of efforts and accomplishments during the reporting period. SPD collects and compiles information reported by each site to develop DOE’s Annual Sustainability Report, Climate Adaptation & Resilience Plan, and Annual Energy Management Report to Congress. The agency goal has been to lower the reporting burden for sites and increase and improve the consistency of information available to decision makers, allowing them to better identify projects and potential for increased efficiency, as well as to reduce waste, lower emissions, and enhance operational resilience. Sites may elect to produce a more polished publication for their leadership and stakeholders, but this step is no longer required. The ORNL SSP narrative report (this document) and the reporting of DOE SPD Sustainability Dashboard performance data is a collaborative effort of approximately 30 subject matter experts (SMEs) from ORNL facility management and research divisions. Annually, these associates come together to provide a report that can be used by DOE to demonstrate continued agency progress in energy efficiency and sustainable federal operations.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

A suberized exodermis is required for tomato drought tolerance

Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Basis for Dose and Reactor Safety Design Criteria for Army Regulation AR 50–7 and DA Pamphlet

This report describes the basis used to develop the radiological dose acceptance and design criteria contained in the draft updates to Army Regulation 50–7 (AR 50–7) Army Reactor Program and its accompanying draft Department of the Army (DA) Pamphlet (PAM), Army Reactor Program Procedures. These criteria will apply to Army nuclear reactors that fall under AR 50–7 and its accompanying DA PAM and ensure alignment with the overall objectives of the Army Reactor Program. The development basis for the radiological dose and design criteria supports a modern, technology-neutral, risk-informed, and performance-based approach to Army regulation of reactors and the demonstration of “adequate protection of the public.” To establish these criteria that support the Army’s unique operational requirements, multiple well-known and well-established standards and their supporting documentation were reviewed to ensure consistency with existing regulatory safety levels, including guidance from U.S. and international sources. These include the U.S. Nuclear Regulatory Commission’s (NRC’s) regulations and policy, the Canadian Nuclear Safety Commission’s (CNSC’s) regulatory documents, the International Atomic Energy Agency’s (IAEA’s) safety standards, as well as industry input that is tailored specifically to advanced microreactors. This report walks through the key definitions and associated references used for these criteria, which are outlined in Section 2.0. Based on these definitions, the dose acceptance criteria were established for various receptors for routine reactor operations (Section 3.2), design basis accidents (Section 3.3), and beyond design basis accidents (Section 3.4). Comparisons of multiple national and international dose limits are provided in these sections. Lastly, Section 4.0 outlines the reactor safety design criteria contained in the draft DA PAM and their associated bases.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Monitoring Plan for the Idaho National Laboratory Remote Handled Low Level Waste Disposal Facility

This monitoring plan for Idaho National Laboratory’s Remote-Handled Low Level Waste Disposal Facility was developed to meet the requirements for monitoring low-level waste disposal facilities according to the U.S. Department of Energy (DOE) Order 435.1, “Radioactive Waste Management,” and the guidance provided in the associated technical standard “Disposal Authorization Statement and Tank Closure Documentation” (DOE-STD-5002-2017). The purpose of this monitoring plan is to document a monitoring strategy that includes (1) compliance monitoring activities to demonstrate compliance with regulatory standards/limits and (2) performance monitoring to build confidence the facility is performing as demonstrated in the facility performance assessment (PA) (DOE-ID 2018a), composite analysis (CA) (DOE ID 2012), and CA addendum (DOE-ID 2018b). The de minimus impact to the aquifer predicted by the PA suggests that aquifer compliance monitoring should be augmented with performance monitoring of the drainage course materials and sedimentary interbeds in the vadose zone beneath the facility to provide a more effective means of identifying performance deviations. The monitoring approach delineated in this document was informed by the systems evaluation of natural and engineered facility features presented in the PA, an assessment of aquifer baseline conditions (INL 2017d), the dose analysis conducted in support of the PA and CA, and monitoring data collected during the first four years of facility operations (baseline monitoring phase) (INL 2023b). This plan provides monitoring locations, sampling frequencies, and sampling methods; recommendations for data evaluation; and a description of the monitoring plan implementation. Collected data will be used to demonstrate facility compliance and to identify conditions that are not consistent with the key assumptions made by the PA and CA.

12 - MGMT OF RADIOACTIVE AND NON-RADIOACTIVE WASTE↗
DOE OSTI2025

Supporting New Advanced Nuclear Technologies for Commercial-Maritime Applications

The ANS summary doesn't require an abstract, but I will produce one for the purpose of LRS: The large demand for maritime nuclear power underscores the need for experimental campaigns and modeling and simulation of new advanced reactors, which offer numerous advantages in terms of safety, efficiency, and compactness. INL, through the work conducted by NRIC and ABS, has addressed some of the technical, regulatory, and economic aspects of potential nuclear commercial maritime applications. However, on the technical side, there remain important physical phenomena, particularly for advanced reactors, that are not yet fully understood. Addressing these knowledge gaps requires a combination of experiments and advanced modeling and simulation techniques. INL possesses significant expertise in Multiphysics modeling and simulation. By collaborating with INL, the maritime nuclear sector can leverage this expertise to advance the development and deployment of innovative nuclear technologies.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Field Testing of Safeguards Technologies in the Hot Fuel Examination Facility

Recent developments in nuclear fuel reprocessing techniques have yielded more efficient processes and fuel cycle options that strengthen the nuclear industry and production of clean energy. One such area of interest is pyroprocessing of used oxide fuel. However, with these advances in the back end of the nuclear fuel cycle, advances in safeguards instrumentation, measurements, and approaches are needed to ensure special nuclear material (SNM) is accounted for according to regulatory requirements. As a high-level overview of a nominal pyroprocessing approach, used oxide fuel from commercial light water reactors (LWR) is mechanically removed from the metallic cladding. Then the fuel is crushed and randomized representative samples are taken and sent to an analytical lab for analysis. The analytical results of the feed material are used for input accountancy into the rest of the process. The crushed oxide fuel is then moved to the oxide reduction (OR) furnace where it is reduced from an oxide to metallic form. The OR product is distilled to remove salt and then moved to an electrorefiner (ER), where it is immersed in a eutectic mixture of lithium chloride potassium chloride (LiCl-KCl) that typically ranges between 450-550 ?. Within the ER, the usable uranium is electrochemically transported through the molten salt from the anode to the cathode, and then subsequently removed as a relatively pure U product.. A simplified model of pyroprocessing techniques with added emphasis on the safeguards can be seen below in Fig. 1

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction

TRIMER, Transcription Regulation Integrated with MEtabolic Regulation, is a genome-scale modeling pipeline targeting at metabolic engineering applications. Using TRIMER, regulated metabolic reactions can be effectively predicted by integrative modeling of metabolic reactions with a Transcription Factor (TF)-gene regulatory network (TRN), which is modeled via a Bayesian network (BN). In this paper, we focus on sensitivity analysis of metabolic flux prediction for uncertainty quantification of BN structures for TRN modeling in TRIMER. We propose a computational strategy to construct the uncertainty class of TRN models based on the inferred regulatory order uncertainty given transcriptomic expression data. With that, we analyze the prediction sensitivity of the TRIMER pipeline for the metabolite yields of interest. The obtained sensitivity analyses can guide Optimal Experimental Design (OED) to help acquire new data that can enhance TRN modeling and achieve specific metabolic engineering objectives, including metabolite yield alterations. Here we have performed small- and large-scale simulated experiments, demonstrating the effectiveness of our developed sensitivity analysis strategy for BN structure learning to quantify the edge importance in terms of metabolic flux prediction uncertainty reduction and its potential to effectively guide OED.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and $K_a$/$K_s$ ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

59 BASIC BIOLOGICAL SCIENCES↗