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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
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 OSTI2023

Top-Down Proteomics of Mouse Islets With Beta Cell CPE Deletion Reveals Molecular Details in Prohormone Processing

Altered prohormone processing, such as with proinsulin and pro-islet amyloid polypeptide (proIAPP), has been reported as an important feature of prediabetes and diabetes. Proinsulin processing includes removal of several C-terminal basic amino acids and is performed principally by the exopeptidase carboxypeptidase E (CPE), and mutations in CPE or other prohormone convertase enzymes (PC1/3 and PC2) result in hyperproinsulinemia. A comprehensive characterization of the forms and quantities of improperly processed insulin and other hormone products following Cpe deletion in pancreatic islets has yet to be attempted. In the present study we applied top-down proteomics to globally evaluate the numerous proteoforms of hormone processing intermediates in a β-cell-specific Cpe knockout mouse model. Increases in dibasic residue–containing proinsulin and other novel proteoforms of improperly processed proinsulin were found, and we could classify several processed proteoforms as novel substrates of CPE. Interestingly, some other known substrates of CPE remained unaffected despite its deletion, implying that paralogous processing enzymes such as carboxypeptidase D (CPD) can compensate for CPE loss and maintain near normal levels of hormone processing. In summary, our quantitative results from top-down proteomics of islets provide unique insights into the complexity of hormone processing products and the regulatory mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Discrete Fracture Network Modeling to Estimate Upscaled Parameters for the Topopah Spring, Lava Flow, and Tiva Canyon Aquifers at Pahute Mesa, Nevada National Security Site

This report describes the results of Discrete Fracture Network (DFN) simulations for the Topopah Spring Aquifer (TSA), Lava Flow Aquifer, and Tiva Canyon Aquifer (TCA), at Pahute Mesa on the Nevada National Security Site (NNSS), formerly the Nevada Test Site. The research focuses on calculating upscaled groundwater flow and contaminant transport parameters using DFNs generated according to fracture characteristics observed in the TSA, LFA and TCA at Pahute Mesa. The highly fractured and heterogeneous nature of these aquifers makes them candidates for stochastic DFN modeling of radionuclide transport on a small scale with subsequent upscaling. One hundred independent DFN realizations are generated for each aquifer, and the upscaled parameters for continuum simulations of subsurface flow and transport in fractured media at Pahute Mesa are calculated. Our goal is to implement a modeling approach that can translate parameters to larger-scale models that account for local-scale flow and transport processes, such as channelization of flow and transport along a few well connected, large fractures. Additionally, to simulate advective and advective-diffusive transport through the fracture networks, the Time Domain Random Walk (TDRW) approach is applied to account for matrix diffusion into a finite half-space. Moreover, a novel approach to calculate dynamic (active) fracture surface area to reflect flow channeling is implemented. This work will improve the representation of radionuclide transport processes in largescale, regulatory-focused models by providing estimates of hard-to-measure flow and contaminant transport parameters at large scales. In this report, we (1) show recent results of flow and transport simulations on multiple DFN realizations of the TSA, LFA, TCA; (2) discuss the resulting distributions of estimated upscaled parameters; (3) describe the estimation of upscaled parameters for an equivalent parallel-plate continuum model and (4) present a comparison between simulated transport from the equivalent continuum model and an actual DFN.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Preliminary Thermal-Hydraulic Analysis of the UTA–2 Subcritical Linear Accelerator–Driven System

The National Nuclear Security Administration’s mission includes establishing a reliable supply of 99 Mo without highly enriched uranium. Oak Ridge National Laboratory (ORNL) supports this objective through collaborative research and development with industrial partners. Niowave Inc., a current partner, is currently designing a subcritical linear accelerator-driven system (ADS) and preparing for the US Nuclear Regulatory Commission’s licensing process. Niowave’s system has the potential to efficiently supply medical radioisotopes. The technology includes a superconducting electron accelerator and a pile of both natural and low-enriched uranium (LEU) targets. The process fissions uranium and many valuable isotopes can then be extracted from the targets. Niowave is currently iterating through conceptual and detailed design processes for several system sizes. This report discusses UTA–2, which is at the demonstration stage. UTA–2 will validate numerical modeling results with experimental measurements before progressing to the detailed design of UTA–3, the commercial-sized ADS. The thermal-hydraulic behavior of the UTA–2 core design was numerically investigated using STAR-CCM+, as described in this report. STAR-CCM+, a state-of-the-art computational fluid dynamics (CFD) software that was commercially developed by Siemens, has an extensive user base and a set of validation studies. It is also compliant with the American Society of Mechanical Engineers’ Nuclear Quality Assurance 1 standard. Three cases are investigated in this report. Case 1 quantified the temperature field within the UTA–2 assembly and water tank using only conduction as the method of thermal energy transport. This simplified approach was overly conservative and yielded wetted cladding temperatures above the coolant saturation temperature. In this case, the maximum temperature of the wetted cladding surface of the highest power rod exceeded the saturation temperature of water by 63.8°C. Because of the overly conservative approach taken in Case 1 and its negative subcooled margin, buoyancy-driven natural circulation flow physics were implemented in Case 2. Adding coolant motion significantly distributed the thermal energy of the system through convective heat transfer. This relatively small amount of convective heat transfer significantly reduced system temperatures and increased the subcooled margin from –63.8 to 61.3°C. This margin confirmed that no boiling was expected during normal operation of UTA–2 at 230 W. Case 3 had no additional physics models but considered an overpower event during which the power of each LEU and natural uranium rod was at its respective peak values. This resulted in a study with the total assembly power equal to 176% of the nominal power of 230 W considered in Cases 1 and 2. The resulting natural circulation flows were slightly enhanced. The subcooled margin decreased slightly to 46.3°C, which is still a significant margin to local boiling of the water within the tank. This margin confirmed that no boiling was expected during an abnormal operation of UTA–2 at 406 W.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2026

The Role of the U.S. Electric Distribution System in Serving Data Center and Other Large Loads

The rapid expansion of data centers in the United States is reshaping how the electric distribution system must plan for and accommodate large load interconnections. This report evaluates the role of the distribution grid in serving these loads, from small edge facilities to hyperscale campuses. Using national datasets, utility filings, and industry studies, we assess demand growth, reliability requirements, interconnection thresholds, and infrastructure needs at substations and feeders. The analysis highlights the mismatch between fast data center development timelines and slower utility planning and construction cycles, as well as strategies such as phased energization, on-site generation, hosting capacity maps, and structured interconnection frameworks. While focused on data centers, the insights also apply to other high-density loads such as advanced manufacturing, hydrogen production, and electrified transportation. The report concludes with approaches to align planning processes, transparency tools, and regulatory frameworks so utilities can manage new large loads in ways that support a reliable and resilient grid.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Understanding the Environmental Study Life Cycle in the United States Hydropower Licensing and Federal Authorization Process

We analyzed United States Federal Energy Regulatory Commission (FERC) documents prepared for 29 recently licensed hydropower projects and created two novel datasets to improve understanding of the environmental study life cycle, defined here as the process that begins with an environmental study being requested by a hydropower stakeholder or regulator, and ends with the study either being rejected or approved/conducted. Our two datasets consisted of summaries of information taken from (1), study determination letters prepared by FERC for 23 projects that were using the integrated licensing process, and (2), environmental study submittals and issuances tracked and attributed to seven projects using the FERC record. Our objective was to use the two resulting environmental life cycle datasets to understand which types of environmental studies are approved, rejected, and implemented during FERC licensing, and how consistently those types of studies are required across multiple hydropower projects. We matched the requested studies to a set of 61 river function indicators in eight categories and found that studies related to the category of biota and biodiversity were requested most often across all 29 projects. Within that category, studies related to river function indicators of presence, absence, detection of species and habitat/critical habitat were the most important to stakeholders, based on the relative number of studies requested. The study approval, rejection, and request rates were similar within each dataset, although the 23 projects with study determination letters had many rejected studies, whereas the dataset created from the seven projects had very few rejected studies.

13 HYDRO ENERGY↗
DOE OSTI2022

BETO 2021 Peer Review: Algae Biotechnology Partnership - Technology Area Session: Advanced Algae Systems

Development of advanced genetic and genomic tools for targeted algal metabolic engineering pursuits will be integral to achieving target biomass productivity and, ultimately, the BETO goal of cost-competitive biofuels derived from algal biomass by 2022. However, at present, broad-host-range tool development is currently hindered by strain-specific negative regulatory mechanisms. Indeed, the biological processes controlling algal transcription and translation are subject to complex host regulation, which often presents hurdles for targeted genetic engineering strategies. Advanced genetic approaches offer a means to rewire these regulatory systems and/or introduce novel functionality into algal biocatalysts. Synthetic systems biology approaches also present a means to construct novel genetic regulatory networks and rewire natural biological systems to establish an “orthogonal central dogma,” wherein non-native control elements are introduced into or evolved in host microbes for bypass of host control. To this end, the Algae Biotechnology Partnership aims to develop advanced genetic editing tools and synthetic and orthogonal genetic regulatory systems to enable universal metabolic engineering strategies in top-candidate deployment algal strains. Successful development will ultimately open the door for targeted strain-engineering strategies, aimed at maximizing algal outdoor biomass production, composition, and strain robustness.

biocatalysis↗
DOE OSTI2025

Reassessment of caustic scrubbing for radioiodine capture during UNF processing

The effective removal of iodine-129 from gaseous emissions during used nuclear fuel processing is critical for minimizing environmental contamination and ensuring environmental regulatory compliance. Recent research has focused on optimizing process air, scrubber conditions, and integrating complementary techniques, such as solid sorbents as a polishing step, to improve iodine capture efficiency. The efficiency of a caustic scrubber is influenced by several factors, such as pH, temperature, gas–liquid contact time, and the presence of oxidants, yet the existing literature tends not to consider how these factors might interact or change in importance with process scaling. This perspective advocates for reconsidering how to mitigate many of these factors, especially in view of the transition from laboratory bench to pilot scale and beyond. This paper reviews the principles, operational parameters, and advancements in caustic aqueous scrubbing for radioiodine mitigation, aims to direct the next scientific pursuit of this technology, and inform environmental decision-making.

Ngelale, Randy [Oak Ridge National Laboratory (ORN↗
DOE OSTI2021

Hazardous Chemical Inventory Guidelines, Purpose, and Process

The Environment, Safety, and Health Planning department at Sandia National Laboratories is interested in the purchase and storage of chemicals and their potential impact following an uncontrolled release. The large number of projects conducted at SNL make tracking every chemical purchase impractical; therefore, attention is focused on hazardous substances purchased in large quantities. Chemicals and quantities of concern are determined through regulatory guidelines; e.g., the OSHA Process Safety Management list, the EPA Risk Management Plan list, and the Department of Energy Subcommittee on Consequence Assessment and Protective Actions Emergency Response Planning Guidelines. Based on these regulations, a list of chemicals with quantities of concern was created using the Aerial Locations of Hazardous Atmospheres (ALOHA) and SCREEN View chemical dispersion modelling software. The nature of this report does not draw conclusions, rather it documents the logic for a chemicals of concern list to ensure compliance with various regulations and form the basis for monitoring chemicals that may affect hazard classification. Hazardous Chemical Inventory Guidelines, Purpose, and Process 4 This page left blank.

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

Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data

Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division. However, identifying how this network regulates the timing of these patterns, including important interactions and regulatory motifs, remains a challenging task. Results We employed four in vivo and in vitro regulatory data sets to investigate the regulatory basis of expression timing and phase-specific patterns cell-cycle expression in Saccharomyces cerevisiae . Specifically, we considered interactions based on direct binding between TF and target gene, indirect effects of TF deletion on gene expression, and computational inference. We found that the source of regulatory information significantly impacts the accuracy and completeness of recovering known cell-cycle expressed genes. The best approach involved combining TF-target and TF-TF interactions features from multiple datasets in a single model. In addition, TFs important to multiple phases of cell-cycle expression also have the greatest impact on individual phases. Important TFs regulating a cell-cycle phase also tend to form modules in the GRN, including two sub-modules composed entirely of unannotated cell-cycle regulators ( STE12-TEC1 and RAP1-HAP1-MSN4 ). Conclusion Our findings illustrate the importance of integrating both multiple omics data and regulatory motifs in order to understand the significance regulatory interactions involved in timing gene expression. This integrated approached allowed us to recover both known cell-cycles interactions and the overall pattern of phase-specific expression across the cell-cycle better than any single data set. Likewise, by looking at regulatory motifs in the form of TF-TF interactions, we identified sets of TFs whose co-regulation of target genes was important for cell-cycle expression, even when regulation by individual TFs was not. Overall, this demonstrates the power of integrating multiple data sets and models of interaction in order to understand the regulatory basis of established biological processes and their associated gene regulatory networks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Workshop on Establishing and Operating a National Nuclear Security Support Centre Hypothetical Scenario: “Centralia Nuclear Security Support Centre Strategy Implementation Plan”

[This is part of a hypothetical scenario-based exercise for workshop participants, based on the fictitious country "Centralia."] In prior years, as a part of efforts to strengthen and better sustain nuclear security within the State, Centralia requested through the Integrated Nuclear Security Support Plan (INSSP) framework that the International Atomic Energy Agency (IAEA) conduct an expert mission on establishing and operating a national nuclear security support centre (NSSC). After the IAEA conducted the NSSC expert mission, members of the Centralia Committee on Nuclear Security (CNS) agreed to initiate the feasibility determination phase of establishing an NSSC, in line with the systematic process recommended by the IAEA. Centralia Nuclear Regulatory Authority (CNRA), as the designated lead organization for coordinating the feasibility determination process, prepared a Feasibility Report in collaboration with members of the CNS and based on input gathered among relevant national stakeholders. The report was presented to the National Security Advisor (NSA), who reviewed and approved the proposal for Centralia to proceed with establishing an NSSC. After Centralia moved into the planning phase for the Centralia Nuclear Security Support Centre (CNSSC), per REF, the primary stakeholders of the centre jointly developed this strategy implementation plan, which provides an outline of the organizational structure, needs analysis, programme objectives, financial and project management, risk management, and other key aspects of the centre. This document will be reviewed and updated as necessary on a semi-annual basis during the project implementation period of establishing CNSSC.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Safeguards Modeling for Advanced Nuclear Facility Design.

Future nuclear fuel cycle facilities will see a significant benefit from considering materials accountancy requirements early in the design process. The Material Protection, Accounting, and Control Technologies (MPACT) working group is demonstrating Safeguards and Security by Design (SSBD) for a notional electrochemical reprocessing facility as part of a 2020 Milestone. The idea behind SSBD is to consider regulatory requirements early in the design process to provide more optimized systems and avoid costly retrofits later in the design process. Safeguards modeling, using single analyst tools, allows the designer to efficiently consider materials accountancy approaches that meet regulatory requirements. However, safeguards modeling also allows the facility designer to go beyond current regulations and work toward accountancy designs with rapid response and lower thresholds for detection of anomalies. This type of modeling enables new safeguards approaches and may inform future regulatory changes. The Separation and Safeguards Performance Model (SSPM) has been used for materials accountancy system design and analysis. This paper steps through the process of designing a Material Control and Accountancy (MC&A) system, presents the baseline system design for an electrochemical reprocessing facility, and provides performance metrics from the modeling analysis. The most critical measurements in the electrochemical facility are the spent fuel input, electrorefiner salt, and U/TRU product output measurements. Finally, material loss scenario analysis found that measurement uncertainties (relative standard deviations) for Pu would need to be at 1% (random and systematic error components) or better in order to meet domestic detection goals or as high as 3% in order to meet international detection goals, based on a 100 metric ton per year plant size.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2022

Using Systems Theoretic Process Analysis and Causal Analysis to Map and Manage Organizational Information to Enable Digitalization and Information Automation

The overarching goal of this Light Water Reactor Sustainability Program–supported research and development project is to provide planning tools and comprehensive guidance to utilities considering or undertaking full nuclear plant modernization. The results of this research will provide the nuclear industry with a comprehensive and usable solution, including guidance, lessons learned, methods, and planning tools. This research is currently working to provide guidance on digitalization and information automation to enable the evolution of data to information, insight, and action—thereby allowing utilities to operate safely and cost-competitively with all other electrical generation sources. Light Water Reactor Sustainability Program researchers have also recently started investigating how human and technology integration principles, information automation, and digitalization enable data evolution. These researchers are currently in the process of validating the use of System-Theoretic Process Analysis to define high-level safety constraints in the United States Nuclear Regulatory Commission’s problem identification and resolution process (i.e., a plant compliance information gathering activity). The next step in this research, which is described in the following sections of this report, is to map out data evolution in a use case to identify inefficiencies in another aspect of plant compliance information gathering and communication activities—event investigations and root cause analyses.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2026

U.S. Hydropower Relicensing and License Surrender Data and Metadata, 2026

The U.S. Hydropower Relicensing and License Surrender Database (2026) provides a comprehensive, nationwide snapshot (as of December 31, 2025) of hydropower projects across the United States that are undergoing Federal Energy Regulatory Commission (FERC) relicensing or license surrender processes. Compiled by Oak Ridge National Laboratory, the dataset includes detailed project-level attributes such as geographic location, ownership type, waterway, project type (hydropower or pumped storage), regulatory milestones (e.g., Notice of Intent, application dates, FERC issuance dates), licensing process type (ILP, TLP, ALP), operational characteristics, capacity changes, settlement agreements, construction or turbine‑generator investments, and project status categories spanning relicensing, surrenders, exemptions, and terminations. Together, the relicensing and surrender records offer a detailed view of regulatory trends, infrastructure transitions, dam removals, and economic drivers influencing the evolution of the U.S. hydropower fleet.

Johnson, Megan [ORNL] (ORCID:0000000290141741)↗
DOE OSTI2021

FAT10 promotes the progression of bladder cancer by upregulating HK2 through the EGFR/AKT pathway

Highlights: • FAT10 and HK2 expression are both up-regulated in BC tissues. • FAT10 promotes the Warburg effect and progression of BC cells by HK2. • FAT10 regulates cell progression in HK2-dependent manner through EGFR/AKT pathway in bladder cancer. • FAT10 directly interacts with EGFR and inhibits its ubiquitination and stabilizes EGFR. The ubiquitin-like protein FAT10 and the hexokinase protein HK2 play vital regulatory roles in several cellular processes. However, the relationship between these two proteins and their role in the pathogenesis of bladder cancer are not well understood. Here, we found that FAT10 and HK2 protein levels were markedly higher in bladder cancer tissues than in normal adjacent tissues. In addition, RNAi-mediated silencing of FAT10 led to reduced HK2 levels and suppressed bladder cancer progression in vivo and in vitro. The results of our in vivo and in vitro experiments revealed that HK2 is critical for FAT10-mediated progression of bladder cancer. The current study demonstrated that FAT10 enhanced the progression of bladder cancer by positively regulating HK2 via the EGFR/AKT pathway. Based on our findings, FAT10 is believed to stabilize EGFR expression by modulating its degradation and ubiquitination. The results of the current study indicate that there is a correlation between FAT10 and HK2 in the progression of bladder cancer. In addition, we identified a new pathway that may be involved in the regulation of HK2. These findings implicate dysfunction of the FAT10, EGFR/AKT, and HK2 regulatory circuit in the progression of bladder cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Innovative Strategies for Long-Term Monitoring of Complex Groundwater Plumes at DOE’s Legacy Sites (Workshop Report)

Most remaining Department of Energy (DOE) sites will require extended periods of institutional control, especially at complex groundwater sites where attenuation-based strategies have been implemented to facilitate closure. The current practice of monitoring—obtaining and analyzing contaminant concentration in groundwater samples at numerous wells—will account for a large portion of the projected life-cycle at these DOE sites unless a new approach is adopted. State-of-the-art technologies are being developed, including in situ sensors, geophysics, radiation mapping, numerical modeling and AI/ML. These technologies can optimize monitoring strategies in space and time, provide spatially extensive information at vulnerable regions and/or provide more continuous monitoring at lower cost. As part of DOE’s Office of Environmental Management (DOE-EM’s) efforts to advance long-term monitoring systems, an in-person/virtual hybrid workshop was hosted by Savannah River National Laboratory (SRNL) on January 24 and 25, 2023, in Augusta, Georgia. Because DOE-EM’s complex sites will eventually be transferred to DOE’s Office of Legacy Management (DOE-LM), representatives of DOE-LM were important participants in the workshop. The purpose of the workshop was to identify challenges and opportunities for deploying advanced technologies for long-term monitoring at DOE sites. The key questions during the workshop were: 1) the regulatory acceptance of replacing a process that traditionally has used laboratory sampling and analysis of groundwater samples, and 2) the application of this strategy to the southwestern arid sites that include many of the remaining DOE-EM and DOE-LM complex groundwater plumes. Characteristics common to most arid sites present both limitations and opportunities for advanced technologies. DOE-EM has funded a National Laboratory team from SRNL, Lawrence Berkeley National Laboratory (LBNL), and Pacific Northwest National Laboratory (PNNL) to establish the overarching framework of long-term monitoring by systematically combining advanced hardware and software technologies. This project is titled “Advanced Long-Term Environmental Monitoring Systems (ALTEMIS)” and is sponsored by the DOE-EM Technology Development Program. The multi-laboratory team is currently developing and testing innovative monitoring strategies, including the use of in situ groundwater sensors, geophysics, drone/satellite-based remote sensing, reactive transport modeling, and artificial intelligence/machine learning (AI/ML). The project’s demonstration testbed is at the Savannah River Site (SRS) F-Area Seepage Basins, where a well-characterized complex groundwater plume composed of uranium and other radionuclides is in the latter stages of remediation. The workshop included more than 70 participants, presentations, a field visit to F-Area, breakout working groups, and large group discussion. Participants developed recommendations on five topics: in situ sensors, spatially integrative tools, challenges to regulatory acceptance, AI/ML strategies, and transitioning sites to DOE-LM.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus

Abstract Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.

Biochemistry & Molecular Biology↗
DOE OSTI2023

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli

ABSTRACT The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made toward identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N = N-R’), found in diverse chemicals in both food and drugs. Surprisingly, the canonical azoR gene in Escherichia coli was dispensable for azo bond reduction. Instead, azoreductase activity was controlled by the fumarate and nitrate reduction ( fnr ) regulator, consistent with a requirement for the anoxic conditions found within the gastrointestinal tract. Paired transcriptomic and proteomic analysis of the fnr regulon revealed that in addition to altering the expression of multiple reductases, FNR is necessary for the metabolism of L-Cysteine to hydrogen sulfide, enabling the degradation of azo bonds. Furthermore, we found that FNR indirectly regulates this process through the small noncoding regulatory RNA fnrS . Taken together, these results show how gut bacteria sense and respond to their intestinal environment to enable the metabolism of chemical groups found in both dietary and pharmaceutical compounds. IMPORTANCE This work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and nonenzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen, and L-Cysteine control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.

59 BASIC BIOLOGICAL SCIENCES↗