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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

PNNL Review of Federal and State Agency Regulatory Streamlining Practices

All major federal actions that have the potential to significantly affect the environment (e.g., land purchases and/or issuing grants, permits, leases, or licenses) are subject to multiple statutes including the following: • an environmental analysis under the National Environmental Policy Act (NEPA) • potential consultations with the U.S. Fish and Wildlife Service (USFWS) and/or National Marine Fisheries Service (NMFS) under the Endangered Species Act of 1973, as amended (ESA) • potential consultations with State Historical Preservation Officers (SHPOs) and/or tribal nations [often Tribal Historic Preservation Officers (THPOs)] under the National Historic Preservation Act of 1966 (NHPA). Given the size of the federal government and the corresponding variability and complexity in its missions, different branches within the federal government have a fairly wide range of approaches to fulfill their NEPA and consultation requitements. Many of these approaches are founded on the desire to streamline their NEPA and consultation processes while meeting the spirit and letter of the regulations. Some federal and state environmental/engineering agencies have developed web-based dashboards that provide a single web location for permit application submittals. They also use general permits in their various permitting processes. General permits can streamline the permitting process by establishing identical requirements for all eligible applicants. This reduces the time these agencies need to spend reviewing individual permits and setting specific requirements. In addition, general permits do not require a case-specific permit application. This paper presents a sampling of effective agency examples of streamlining the NEPA process and associated agency consultations. It also includes several examples of federal and state agency web portals, online application systems, and general permits that make application processes more efficient and accessible.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa

Plant regeneration is an important dimension of plant propagation and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. Association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants; however, the performance of these methods depends on the accuracy and scale of phenotyping. To enable a large-scale GWAS of in planta callus and shoot regeneration in the model tree Populus, we developed a phenomics workflow involving semantic segmentation to quantify regenerating plant tissues over time. We found that the resulting statistics were of highly non-normal distributions, and thus employed transformations or permutations to avoid violating assumptions of linear models used in GWAS. We report over 200 statistically supported quantitative trait loci (QTLs), with genes encompassing or near to top QTLs including regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. Our results encourage models of hormonal signaling during plant regeneration to consider keystone roles of stress-related signaling (e.g. involving jasmonates and salicylic acid), in addition to the auxin and cytokinin pathways commonly considered. The putative regulatory genes and biological processes we identified provide new insights into the biological complexity of plant regeneration, and may serve as new reagents for improving regeneration and transformation of recalcitrant genotypes and species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

An Advanced Machine Learning and Artificial Intelligence System for Demonstrating Radiation Regulatory Compliance in DOE Accelerator Facilities

In this Phase II proposal, Applied Research LLC (ARLLC), Thomas Jefferson National Accelerator Facility (Jefferson Lab), and Old Dominion University (ODU) propose the combination of domain knowledge (beam characteristics, fixed structural shielding, earthen burden (the soil and foliage added to the dome of the experimental halls as additional shielding), etc.), machine learning (ML) and/or artificial intelligence (AI) to correlate a variety of multi-modal onsite signals and the radiation fields seen in accessible areas of the accelerator site and the site boundary. The ML/AI will consider the complex influence of environmental parameters affecting the radon contribution of the measurements, focusing on actual data obtained from Jefferson Lab. In Phase I, the coded beam and location data were fed into a deep learning model to predict doses at several designated locations in Jefferson Lab’s facility. Moreover, a dense radiation map was generated using only a sparse collection of the samples in a facility. In Phase II, we will develop a software prototype containing a radiation prediction algorithm, dense radiation map algorithms, and background noise prediction algorithms, with actual data used to evaluate the prototype. This work will provide a framework for evaluation of radiation measurement results around the site based on learned responses. In addition, the proposed approach allows more granular mapping of radiation levels. Better understanding and communication of these levels is related to the overall approach in keeping doses to personnel ALARA.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

A Sorghum F-Box Protein Induces an Oxidative Burst in the Defense Against Colletotrichum sublineola

The hemibiotrophic fungal pathogen Colletotrichum sublineola is the causal agent of anthracnose in sorghum ( Sorghum bicolor), resulting in leaf blight, stalk rot, and head blight in susceptible genotypes, with yield losses of up to 50%. The development of anthracnose-resistant cultivars can reduce reliance on fungicides and provide a more sustainable and economical means for disease management. A previous genome-wide association study of the sorghum association panel identified the candidate resistance gene Sobic.005G172300 encoding an F-box protein. To better understand the role of this gene in the defense against C. sublineola, gene expression following infection with C. sublineola was monitored by RNA sequencing in seedlings of sorghum accession SC110, which harbored the resistance allele, and three accessions that harbored a susceptible allele. Only in SC110 did the expression of Sobic.005G172300 increase during the biotrophic phase of infection. Subsequent transcriptome analysis, gene co-expression networks, and gene regulatory networks of inoculated and mock-inoculated seedlings of resistant and susceptible accessions suggest that the increase in expression of Sobic.005G172300 induces an oxidative burst by lowering the concentration of ascorbic acid during the biotrophic phase of infection. Based on gene regulatory network analysis, the protein encoded by Sobic.005G172300 is proposed to target proteins involved in the biosynthesis of ascorbic acid for polyubiquitination through the SCF E3 ubiquitin ligase, causing their degradation via the proteasome.

Plant Sciences↗
DOE OSTI2022

Enhancing Lifetime and Reducing Costs for Fish Diversion Netting Structures (Abstract)

This effort will focus on technology transfer and commercialization of antifouling coatings with an enthusiastic and engaged industrial team. Environmental requirements and operational demands call for a nontoxic coating/paint to prevent fouling on fish passage guidance netting at hydropower facilities. For example, one netting customer estimated the capital cost for compliance at $\$12$ million to $\$15$ million. This project will build partnerships between PNNL and private companies to optimize, demonstrate, mature, and commercialize a novel PNNL-developed technology that addresses this critical coating need of the hydropower industry. This effort will support modification of existing coatings for application to flexible netting structures. Industrial partners include commercial coating development specialist (Lorama), hydrophobic material manufacturer and paint developer (Dry Surface Technologies), aquatic applications specialists (Prometheus Innovations and River Connectivity Systems), and hydropower netting producer (Pacific Netting Products). Engagement with the U.S. Army Corps of Engineers (USACE) and Bureau of Reclamation (BOR), two hydropower operators, throughout the project will provide expertise and field test sites that will provide crucial proof of real-world performance data (additional details provided in Teaming section). Taylor Shellfish Farms will provide organisms and fouling expertise as well as a perspective of potential broader impacts for the blue economy. Sample netting will demonstrate performance in a range of environments for key hydropower applications. PNNL will work with industrial partners to overcome commercialization barriers as well as resolving any manufacturing or regulatory issues. This Phase 1 effort is focused on technology optimization for application to fish passage guidance netting and technology validation as verified by independent testing (through USACE, BOR, Taylor Shellfish and Prometheus Innovations). Through this effort, SLIC will be demonstrated for netting applications at technology readiness level (TRL) 5. The field test data will allow optimization of SLIC formulation and performance which is key to enabling technology transfer of a mature proven technology to industry and production of a viable commercial product specifically focused for hydropower needs.

13 HYDRO ENERGY↗
DOE OSTI2022

Net-zero Microgrid Program Report: Microrred de la Montaña Feasibility Study (Executive Summary Extended)

This feasibility study provides the technical and economic rationale for the Microrred de la Montaña as a viable solution for supplying reliable and resilient electricity to an underserved region in Puerto Rico – a region that is the first to be disconnected from the grid and the last to be restored, enduring months long outages. It begins the process of the development of the microgrid through conceptual design, engineering, detailed electrical design, implementation, and operation. The Microrred de la Montaña is organized under the governance of the Cooperativa Hidroeléctrica de la Montaña (Cooperativa) which has legal status as a cooperative and power provider under the laws of Puerto Rico. The members are the municipalities of Adjuntas, Jayuya, Lares and Utuado with a combined population of 90,000. These municipalities are in central Puerto Rico – a mountainous region that is extremely vulnerable to weather events and excessive, long-duration power outages and are among the poorest and most disadvantaged regions in Puerto Rico. Funding from external sources is necessary to acquire the resources for a resilient power delivery system. Regulatory support is necessary to establish operational relationships with the incumbent power providers. The Microrred de la Montaña is envisioned as a resilient microgrid that manages distributed energy resources – local solar, storage, and hydroelectricity over an upgraded distribution network within the boundaries of four municipalities. This feasibility study provides the results of an extensive techno-economic analysis to form a sound basis for decision-making by community leaders, their constituents, funding and investment agencies, and regulators to realize the benefits that are achievable by fully implementing the design and planning recommended for the Microrred de la Montaña.

13 HYDRO ENERGY↗
DOE OSTI2024

Jackson, L., Johnson, M.B., Latrach, A., Grimes, D., Martinez, C., and Mclaughlin, J.F., 2024, Multidisciplinary geotechnical data collection, curation, and analysis for conformity with the regulatory framework for geologic carbon storage in Wyoming, USA: Geological Society of America Abstracts with Programs. Vol. 56, No. 5, 2024, doi: 10.1130/abs/2024AM-405024

Title: Multidisciplinary Geotechnical Data Collection, Curation, and Analysis for Conformity with the Regulatory Framework for Geologic Carbon Storage in Wyoming, USA. Text: Construction and operation of wells for geologic sequestration of carbon dioxide necessitate that they are permitted under the Environmental Protection Agency’s Underground Injection Control Class VI requirements. Class VI wells conform to stringent requirements to ensure long-term safety and integrity of the storage site and the protection of Underground Sources of Drinking Water. Entities pursuing Class VI permitting must provide comprehensive geologic site characterization, including regional geologic structure and stratigraphy, aquifer information, reservoir and confining unit geomechanical properties, geochemical analyses, assessment of trapping capacity and mechanisms, and a variety of other of multidisciplinary geotechnical data. The Wyoming Class VI Site Characterization Database Project is focused on developing a geologic site characterization database of geotechnical information, which has been compiled and verified from established, public databases/entities and scientific literature to expedite Class VI permitting in Sweetwater County within the Greater Green River Basin of southern Wyoming. The preliminary suite of compiled data from 14,000 wells includes 8,000 wells with logs and 7,250 wells with formation tops, ~70 wells with core data (e.g., X-Ray diffraction, petrographic, and petrophysical data), ~2,500 water analyses, ~740 seismic events data, and ~520 bottom-hole temperature measurements. Future work on—and stemming from—this project will include new core analyses, calculation and interpolation of subsurface temperature gradients, mechanical earth models, geochemical simulations, storage capacity estimation, stratigraphic column generation and correlation, and construction of subsurface maps. Finally, this work will help to inspire and facilitate subsurface data compilation and curation beyond Sweetwater County, Wyoming.

42 ENGINEERING↗
DOE OSTI2022

A 100-Mrad (Si) JFET-based Sensing and Communications System for Extreme Nuclear Instrumentation Environments

Dry cask storage is one of two storage methods approved by the U.S. Nuclear Regulatory Commission for spent fuel after removal from reactor cores. Dry casks consist of a stainless steel canister enclosed in a concrete overpack to contain the hazardous radioactive spent fuel rods and provide radiation shielding. Monitoring spent fuel storage casks is desired to ensure the safe containment of the enclosed spent fuel, but is very difficult due to the related harsh temperature and radiation environment. The sensors and associated electronics to monitor temperature, pressure, and/or radiation need to survive high temperatures and radiation doses for extended time periods. For this reason, there is a severe need for radiation-hardened electrical systems that survive well beyond the existing capabilities of commercially available radiation-rated electronic components, which have primarily been developed for space applications. Junction-gate field-effect transistor (JFET) devices are inherently radiation hardened [exceeding 100 Mrad (Si)]. Additionally, when JFETs are used as building blocks for sensing and communication electronics (i.e., oscillators, amplifiers, filters, and mixers), inherently radiation-hardened circuits can be achieved. To this end, JFET-based radiation-hardened electronics interfacing with cask-embedded sensors capable of driving modulated sensor signals through a stainless steel barrier were designed and tested at a dose rate of approximately 500 krad/h (Si) to beyond a 200-Mrad (Si) total ionizing dose. After 200 Mrad (Si), the sensor and communication circuit signals were correctly decoded at the receiver despite oscillator drift. The results from this experiment demonstrate the potential for creating more complex radiation-hardened JFET-based electrical systems for nuclear environments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Building a Collaborative Relationship between Contractor and Oversight at SRPPF

The success of Department of Energy (DOE) projects is dependent on a functional, healthy, and collaborative relationship between the contractor and the federal oversight. A healthy relationship marked by a collaborative mindset between these two groups, can facilitate better operational safety, operational efficiency, and regulatory compliance. This paper will explore aspects of such a relationship, the roles and responsibilities of the contractor and federal oversight, the present and historical relationships in the DOE complex, and best practices considered by the contractor and federal oversight used at the Savannah River Plutonium Processing Facility (SRPPF) at the Savannah River Site (SRS). Due to the current design phase of the SRPPF, the contractor and federal oversight have a unique opportunity to begin establishing a strong relationship early in the project’s life. As a result of this dynamic, the two groups have already demonstrated their ability to successfully respond to ongoing design issues. In general, a strong criticality safety program is beginning to mature for the SRPPF alongside a developing criticality safety federal oversight group. This paper will discuss the various factors that have brought about this collaborative relationship. Lastly, a case study will be incorporated into this paper demonstrating the ability of the SRPPF contractor and federal oversight to overcome challenges relating to the SRPPF project. This case study may guide groups around the DOE Complex to create better, more functional relationships between the two parties. The case study will provide a detailed description of the issue and parties involved, highlight the factors that allowed the group to overcome the challenge via effective collaboration, and the outcome of the event. Increasing collaboration may benefit the complex, as a whole, in order to meet the mission demands of the DOE.

collaboration↗
DOE OSTI2026

Integrating AI Data Centers with the Power Grid

The rapid expansion of artificial intelligence (AI) has triggered an unprecedented surge in electricity demand, with US data center energy use projected to double or triple 2023 levels by 2028. This exponential growth places strain on grid infrastructure, which can hinder timely construction of desired computing capacity. To bridge this supply-demand gap, utilities and AI developers are increasingly turning to demand flexibility, a strategy that incentivizes shifting or reducing power use during peak periods of grid stress. Data centers are uniquely equipped for flexible operations due to their digital workloads, built-in redundancy, and onsite energy assets. This article outlines four primary mechanisms to enable data center flexibility: computational load flexibility (shifting tasks temporally or geographically), flexible use of core facility infrastructure adjustments, energy storage utilization, and onsite electricity generation. To encourage adoption, utilities are deploying new tariff designs, including voluntary interruptible service riders, mandated flexibility requirements, and streamlined interconnection processes for flexible loads. For the highly capitalized and rapidly growing AI industry, the primary motivators for embracing these strategies are expediting facility interconnection, satisfying emerging regulatory mandates, and mitigating community resistance. While demand flexibility cannot substitute the long-term need for new bulk power generation, it serves as an essential, immediate solution for enabling near-term deployment. By transforming data centers from grid stressors into stabilizing assets, flexible operations can ensure reliable grid integration, ease market pressures, and support a resilient power system.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6

The E1 enzyme Uba6 initiates signal transduction by activating ubiquitin and the ubiquitin-like protein FAT10 in a two-step process involving sequential catalysis of adenylation and thioester bond formation. To gain mechanistic insights into these processes, we determined the crystal structure of a human Uba6/ubiquitin complex. Two distinct architectures of the complex are observed: one in which Uba6 adopts an open conformation with the active site configured for catalysis of adenylation, and a second drastically different closed conformation in which the adenylation active site is disassembled and reconfigured for catalysis of thioester bond formation. Surprisingly, an inositol hexakisphosphate (InsP6) molecule binds to a previously unidentified allosteric site on Uba6. Our structural, biochemical, and biophysical data indicate that InsP6 allosterically inhibits Uba6 activity by altering interconversion of the open and closed conformations of Uba6 while also enhancing its stability. In addition to revealing the molecular mechanisms of catalysis by Uba6 and allosteric regulation of its activities, our structures provide a framework for developing Uba6-specific inhibitors and raise the possibility of allosteric regulation of other E1s by naturally occurring cellular metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Optimal operation of multi-plant steam district heating systems for enhanced efficiency and sustainability

Despite their crucial role in supplying heat and power to universities, industries, and healthcare facilities, many steam-based district heating systems rely on outdated control methods. Among these, multi-central plant districts are particularly challenging due to the complexities of coordinating multiple plants, optimizing load distributions, and managing system downtime. In response, new operational strategies are developed to enhance the efficiency and sustainability of steam districts while utilizing existing resources. These strategies include reducing plant operational pressure without compromising the reliable supply to buildings and optimizing load allocation across multiple plants. The load allocation considers boiler part-load efficiency, runtime, network losses, and building pressure set points, and is compared with traditional multi-boiler controls. To support this exploration, new dynamic Modelica models are developed. In addition, methods to reduce modeling complexities are incorporated, enhancing their suitability for practical applications. A holistic district-wide analysis using a real university case study demonstrates a 4.7% fuel savings by lowering boiler operational pressure from 900 kPa to 600 kPa, along with a 13.3% reduction in condensation losses across the distribution network. Furthermore, the load allocation approach results in a 13.1% reduction in fuel consumption during peak winter periods and 15.3% during shoulder periods, with corresponding decreases in carbon emissions and fuel costs. This approach can also save maintenance costs by reducing the boiler runtime by 49.6%. In conclusion, this research underscores the benefits of retrofitting aging steam district heating systems, offering immediate operational improvements by enhancing efficiency, meeting regulatory compliance, and extending infrastructure lifespans while delaying costly overhauls.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Safety-Related Instrumentation and Control Pilot Upgrade (Initial Scoping Phase Implementation Report)

This research report (1) describes the process followed and products developed during the SR I&C Pilot Project Initial Scoping Phase, and (2) captures lessons learned. Exelon Generation and LWRS collaborated to develop a Digital Transformation Strategy as part of a larger Advanced Concept of Operations. The proposed SR I&C Pilot Upgrade provides a foundation stone for this Digital Transformation that will improve plant safety, reliability, and operational performance while lowering plant Total Cost of Ownership (TCO). Initial Scoping Phase activities for this Pilot Project have been performed in accordance with industry processes that have been adapted to better support digital upgrades. These processes include IP-ENG-001, Standard Design Process (SDP), NISP-EN-04, Standard Digital Engineering Process (SDEP), and Electric Power Research Institute (EPRI) Report 3002011816, Digital Engineering Guide (DEG). Completing Initial Scoping Phase Engineering and Operations, Licensing, and Project Management Activities was necessary to sufficiently bound the scope, schedule, and estimated cost of the Project to enable utility management to authorize moving into the Conceptual Design Phase. A significant finding of the Business Case Analysis (BCA) methodology developed and applied as part of this effort was that the growth rate of material costs for sustaining the operation of obsolete SR I&C equipment is accelerating. This directly contributed to the Project Economic Analysis created to justify continuing the Project. Project Initial Scoping Phase lessons learned have also been captured to assist the larger industry in understanding the Digital Transformation Strategy and SR I&C Pilot Project Initial Scoping Phase efforts. This is in keeping with the public/private partnership that has been established between the Department of Energy (DOE) and Exelon for this effort with engagement from the NRC. By addressing first-of-a-kind (FOAK) risks and capturing lessons learned, the SR I&C Pilot Upgrade Project addresses technical, regulatory, and business risks to enable subsequent implementers of similar upgrade.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Safety-Related Instrumentation & Control Pilot Upgrade Initiation Phase Implementation Report

This research report (1) describes the process followed and products developed during the SR I&C Pilot Project Initial Scoping Phase, and (2) captures lessons learned. Exelon Generation and LWRS collaborated to develop a Digital Transformation Strategy as part of a larger Advanced Concept of Operations. The proposed SR I&C Pilot Upgrade provides a foundation stone for this Digital Transformation that will improve plant safety, reliability, and operational performance while lowering plant Total Cost of Ownership (TCO). Initial Scoping Phase activities for this Pilot Project have been performed in accordance with industry processes that have been adapted to better support digital upgrades. These processes include IP-ENG-001, Standard Design Process (SDP) [Reference 2], NISP-EN-04, Standard Digital Engineering Process (SDEP) [Reference 3], and Electric Power Research Institute (EPRI) Report 3002011816, Digital Engineering Guide (DEG). Completing Initial Scoping Phase Engineering and Operations, Licensing, and Project Management Activities was necessary to sufficiently bound the scope, schedule, and estimated cost of the Project to enable utility management to authorize moving into the Conceptual Design Phase. A significant finding of the Business Case Analysis (BCA) methodology developed and applied as part of this effort was that the growth rate of material costs for sustaining the operation of obsolete SR I&C equipment is accelerating. This directly contributed to the Project Economic Analysis created to justify continuing the Project. Project Initial Scoping Phase lessons learned have also been captured to assist the larger industry in understanding the Digital Transformation Strategy and SR I&C Pilot Project Initial Scoping Phase efforts. This is in keeping with the public/private partnership that has been established between the Department of Energy (DOE) and Exelon for this effort with engagement from the NRC. By addressing first-of-a-kind (FOAK) risks and capturing lessons learned, the SR I&C Pilot Upgrade Project addresses technical, regulatory, and business risks to enable subsequent implementers of similar upgrades.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

A tissue‐resolved, network‐based transcriptomic framework for abiotic stress responses in sorghum

Developing climate‐resilient crops requires a detailed understanding of stress‐induced gene expression dynamics, as maladaptive responses can compromise their productivity and survival. Sorghum, a globally important cereal with exceptional tolerance to multiple abiotic stresses, provides a powerful system for investigating these dynamics. However, how stress type, tissue specificity, and temporal progression jointly shape transcriptomic responses in crops remains poorly understood. Here, we present a comparative, time‐resolved transcriptomic atlas of sorghum responses to drought, heat, and salinity stress across shoot and root tissues. Integrative analyses revealed that tissue specificity is the dominant determinant of abiotic stress‐induced gene reprogramming across all three stresses. Building on these global comparisons, we focused on heat stress, as it elicited the most coherent and pronounced transcriptional and regulatory responses, enabling deeper network‐level interrogation. Co‐expression network analysis identified tissue‐specific modules enriched for phytohormone‐responsive genes, while gene regulatory network (GRN) mapping and cistrome analyses uncovered transcription factors (TFs) controlling key hub genes within these modules. Together, this study provides a foundational transcriptomic and network‐based resource for dissecting the regulatory architecture of abiotic stress responses in sorghum and offers prioritized candidates for future functional validation and engineering of climate‐resilient crops.

abiotic stress↗
DOE OSTI2021

Land use and turbine technology influences on wind potential in the United States

As clean energy ambitions have expanded, critically evaluating renewable energy supply has become increasingly important to the energy research community and stakeholders. This study examines the onshore wind resource potential for the conterminous United States and its sensitivity to siting constraints and turbine technology innovation. We compile localized regulatory information and use high-resolution data to present multiple siting regimes covering relatively constrained to unconstrained potentials. Our efforts reveal high sensitivity to these variables and sizable uncertainty in the overall wind energy resource potential. Specifically, we find that siting constraints may shift the total capacity available to commercial wind energy by 2.3–15.1 TW. Furthermore, our results illustrate that technology advancement could require larger setbacks from buildings and infrastructure, reducing the total available capacity potential by 20% relative to estimates using current technology, but that this reduction is largely offset by increased generation such that the net effect on generation is 1%. The observed sensitivity to and uncertainty resulting from the variables we analyze suggest there is value in continued study and development of increasingly sophisticated approaches to characterizing wind resource potential.

14 SOLAR ENERGY↗
DOE OSTI2025

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

Abstract Motivation Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. Results We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. Availability and implementation It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.

Du, Lin (ORCID:0009000289869812)↗
DOE OSTI2020

The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements

Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.

59 BASIC BIOLOGICAL SCIENCES↗