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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Ice Nucleation Measurements during TRACER (Field Campaign Report)

This campaign, Ice Nucleation Measurements during TRACER, was conducted during the TRacking Aerosol Convection Interactions ExpeRiment (TRACER) in Houston, Texas during June-September, 2022. Specifically, our ice nucleation campaign was designed to improve understanding of ice nucleating particles (INPs) and their role in deep convective clouds across the Houston region. Summertime deep convection in southeast Texas is regularly tied to the sea-breeze front (SBF) that pushes inland from the Gulf of Mexico across the region. During TRACER, three Davis Rotating Uniform size-cut Monitors (DRUM; DRUMAir 4-DRUM) were used to collect aerosols for offline ice nucleation measurements in the Brooks laboratory at Texas A&M University. The three instruments were located at the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) first Mobile Facility (AMF1) in La Porte, at the ancillary site in Guy (ANC), and onboard the newly developed Texas A&M Rapid Onsite Atmospheric Measurements Van (ROAM-V). Aerosol at the main ARM TRACER site, ARM1, is expected to arise from local urban, industrial, and ship channel sources. In contrast, the ANC is isolated and rural, and can therefore provide a continental background aerosol population. On select days when convective development was forecast to be probable, ROAM-V commuted from College Station, Texas to Galveston, sampled in the morning/mid-day on the coast, and then transited to a second inland site for the afternoon/evening. Sampling from the ROAM-V allowed us to capture aerosol and meteorological differences between maritime and continental airmasses by strategically positioning the ROAM-V near the coast in the morning in the opposite airmass from the AMF1 site.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Quantifying Capital Cost Reduction Pathways for Advanced Nuclear Reactors

The framework developed in this study is provided both as an excel sheet (https://inl.gov/content/uploads/2023/11/Nuclear-Reactor-Cost-Reduction-Pathway-Spreadsheet-Tool.xlsx) and a Python (Jupyter) Notebook (link: https://github.com/accert-dev/ACCERT/tree/main/Cost%20Reduction). Capital cost considerations are one of the primary inhibitors to the large-scale deployment of nuclear power plants. While it is widely accepted that first units will likely be expensive and relatively uncompetitive, it is reasonable to expect that subsequent units, built in relative quick succession, will be cheaper as they benefit from the so-called “learning effects”. However, the large degree of uncertainty associated with this parameter renders it challenging for first movers to invest in the first few expensive units. To resolve this impasse, the U.S. Department of Energy’s Advanced Nuclear Liftoff study advocated for the formation of large, committed order books of plants of the same technology to spread the costs across several units and kickstart the nuclear supply chain. The study also advocated best practices for avoiding overruns and keeping reactors on budget. This report builds on these key recommendations by attempting to quantify specific pathways toward cost reduction for nuclear energy. A capital cost estimation framework was built to untangle the effect of learning into a subset of key cost drivers, referred to as “levers”. Collectively, the choice of these levers is intended to reflect the decision-making of high-level stakeholders like plant owners and the government. In addition to the size of the firm orderbook, these levers included (a) cost drivers that are most often attributed to cost overruns such as architect/engineering (A/E) proficiency, construction proficiency, procurement service proficiency, design completion prior to the start of construction, and design maturity, and (b) cost reduction strategies such as modular construction, cross-site standardization, safety classification of the reactor building, and of the balance of plant. Two advanced reactor designs were leveraged as use cases and bottom-up cost estimates made with assumptions consistent with a well-executed first-of-a-kind project (WE-FOAK, i.e., almost no overruns) were used as baselines for the models. Cost correlations were surveyed from the literature to determine the impact of important variables on projected timelines and costs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Compaction of crushed salt for safe containment – a summary of the KOMPASS projects

Abstract. For the underground disposal of high-level nuclear waste in rock salt formations, the safety concept includes the backfilling of open cavities with crushed salt. For the prognosis of the sealing function of the backfill for the safe containment of the radioactive waste, it is crucial to have a comprehensive process understanding of the crushed-salt compaction behavior. The crushed-salt compaction process is influenced by internal properties (e.g., grain size, mineralogy, and moisture content) and boundary conditions (e.g., temperature, stress state, and compaction rate) and, therefore, involves several coupled thermal–hydro–mechanical (THM) processes (Hansen et al., 2014; Kröhn et al., 2017). With the paradigm shift from the limited release of radionuclides to safe containment due to the German Repository Site Selection Act passed in 2017, the importance of crushed salt as geotechnical barrier has increased, with a focus on the evolution of its hydraulic properties. Based on the knowledge gaps in the current process understanding, the “Compaction of crushed salt for safe containment” (KOMPASS) projects were initiated to improve the scientific basis behind using crushed salt for the long-term isolation of high-level nuclear waste within rock salt repositories. The efforts to improve the prediction of crushed-salt compaction begun during the first phase of the KOMPASS projects (Czaikowski et al., 2020) and were followed up in a second phase ending in June 2023. The primary achievements of the projects are as follows (Czaikowski et al., 2020; Friedenberg et al., 2022): specification of the KOMPASS reference material, an easily available and reproducible synthetic crushed-salt material, for generic investigations; development of pre-compaction methods and successful production of samples in the short term and under in situ loading conditions; formulation of an extended laboratory program addressing the isolated investigation of known relevant factors influencing the compaction behavior of crushed salt (Düsterloh et al., 2022); execution of long-term compaction tests addressing isotropic and deviatoric load changes, temperature, and compaction state; construction of a backfill body using the KOMPASS reference material in the Sondershausen mine through collaboration with the SAVER (Entwicklung eines salzgrusbasierten Versatzkonzepts unter der Option Rückholbarkeit) project (Schaarschmidt and Friedenberg, 2022); advancement of the tools for microstructure investigation methods (Svensson and Laurich, 2022); generation (first stages) of a microphysical process list combining literature research with our own findings; benchmarking of long-term compaction test for model development and optimization of various existing models as well as the development of new models; application of a virtual demonstrator (2D model representing a backfilled drift in rock salt) for the visualization of developments and the quantification of the models (Rabbel, 2022). In summary, the KOMPASS projects contributed to the reduction of uncertainties and the strengthening of the safety case for using crushed salt within rock salt repositories.

Friedenberg, Larissa↗
NASA NTRS1978

Particle impact tests

Particle impact tests were performed on three types of orbiter surface with a micrometeoroid facility. The test equipment electrostatically accelerated micron sized particles to high velocities simulating micrometeoroid impacts. Test particles were titanium diboride with typical velocities in the range 1 to 2.3 km x sec/1 and equivalent particle diameters in the range 4 to 16 microns. Impact angles to the material surface were 90, 60 and 30 degrees. The particle impact sites were located on the sample surfaces and craters were photographed with a magnification of 400X.

Komatsu, G. K.↗
NASA NTRS1982

Transient processes in metal droplet combustion

Photographic and photometric instrumentation was used to study Al burning in air and in O2 and Zr burning in pure O2. The metals, free-falling and of submillimeter size, were ignited by laser. Occasional coalescence of a cooler oxide follower droplet perturbed and then momentarily quenched the spherically symmetric flame emission and condensation fronts of a Zr droplet. An insoluble molten oxide cap consistently formed and grew on the burning Al droplets, blocking local Al vaporization, and providing a site for further condensation with accompanying heat release. Superheating of the liquid metal at the Al/AlO2 interface then occurs, which can presage metal vapor eruptions. Imposing an acoustic field of 90-130 dB, 1-12 kHz transversely on the combustion zone produced no significant changes in the combustion zone geometry.

Rao Charagundla, S.↗
NASA NTRS1986

Martian dust particles as condensation nuclei - A preliminary assessment of mineralogical factors

Experiments were performed to determine the factors influencing ice nucleation detected in Viking Lander data from the Mars surface. The study focused on the relationship between mineral properties and condensate formation under Mars conditions. Pulverized particles of the primary phases of basaltic rocks and their alteration products, expandable clay minerals and a nonexpandable clay mineral, and petrologically well-characterized regolith materials ranging from 10-60 microns in size, were studied. The powders were individually or in combinations mixed with water in a flowing CO2 atmosphere while calorimetry data was taken on the ice nucleation threshold. The ice-forming characteristics of the mixes were found to be a function of the crystallographic disregistry, chemical bonding, and active-site properties of the individual minerals. The crystalline materials were better nucleators of condensates than were the cryptocrystalline mineral specimens, while nonexpandable clay materials, particularly zeolite, were the more effective nucleators among the weathering product materials.

Gooding, J. L.↗
NASA NTRS1995

Basic principles and recent observations of rotationally sampled wind

The concept of rotationally sampled wind speed is described. The unusual wind characteristics that result from rotationally sampling the wind are shown first for early measurements made using an 8-point ring of anemometers on a vertical plane array of meteorological towers. Quantitative characterization of the rotationally sampled wind is made in terms of the power spectral density function of the wind speed. Verification of the importance of the new concept is demonstrated with spectral analyses of the response of the MOD-OA blade flapwise root bending moment and the corresponding rotational analysis of the wind measured immediately upwind of the MOD-OA using a 12-point ring of anemometers on a 7-tower vertical plane array. The Pacific Northwest Laboratory (PNL) theory of the rotationally sampled wind speed power spectral density function is tested successfully against the wind spectrum measured at the MOD-OA vertical plane array. A single-tower empirical model of the rotationally sampled wind speed is also successfully tested against the measurements from the full vertical plane array. Rotational measurements of the wind velocity with hotfilm anemometers attached to rotating blades are shown to be accurate and practical for research on winds at the blades of wind turbines. Some measurements at the rotor blade of a MOD-2 turbine using the hotfilm technique in a pilot research program are shown. They are compared and contrasted to the expectations based upon application of the PNL theory of rotationally sampled wind to the MOD-2 size and rotation rate but without teeter, blade bending, or rotor induction accounted for. Finally, the importance of temperature layering and of wind modifications due to flow over complex terrain is demonstrated by the use of hotfilm anemometer data, and meteorological tower and acoustic doppler sounder data from the MOD-2 site at Goodnoe Hills, Washington.

Connell, James R.↗
NASA NTRS2000

North Atlantic Aerosol Single Scattering Albedos: TARFOX and ACE-2 Results and Their Relation to Radiative Effects Derived from Satellite Optical Depths

Bergstrom and Russell estimated direct solar radiative flux changes caused by atmospheric aerosols over the mid-latitude North Atlantic Ocean under cloud-free and cloudy conditions. They excluded African dust aerosols, primarily by restricting calculations to latitudes 25-60 N. As inputs they used midvisible aerosol optical depth (AOD) maps derived from AVHRR satellite measurements and aerosol intensive properties determined primarily in the 1996 IGAC Troposheric Aerosol Radiative Forcing Observational Experiment (TARFOX). Those aerosol intensive properties, which included optical depth wavelength dependence and spectra of single scattering albedo (SSA) and scattering asymmetry parameter, were also checked against initial properties from the 1997 North Atlantic Aerosol Characterization Experiment (ACE 2). Bergstrom and Russell investigated the sensitivity of their derived flux changes to assumed input parameters, including midvisible AOD, SSA, and scattering asymmetry parameter. Although the sensitivity of net flux change at the tropopause to SSA was moderate over the ocean (e.g., a SSA uncertainty of 0.07 produced a flux-change uncertainty of 21%), the sensitivity over common land surfaces can be much larger. Also, flux changes within and below the aerosol layer, which affect atmospheric stability, heating rates, and cloud formation and persistence, are quite sensitive to aerosol SSA. Therefore, this paper focuses on the question: "What have we learned from TARFOX and ACE 2 regarding aerosol single scattering albedo?" Three techniques were used in TARFOX to determine midvisible SSA. One of these derived SSA as a best-fit parameter in comparing radiative flux changes measured by airborne pyranometer to those computed from aerosol properties. Another technique combined airborne measurements of aerosol scattering and absorption by nephelometer and absorption photometer. A third technique obtained SSA from best-fit complex refractive indices derived by comparing vertical profiles of lidar backscatter, sunphotometer extinction, and relative size distribution. In ACE 2 midvisible SSA was determined both as a best-fit parameter in comparing measured and calculated flux changes at the surface and by combining nephelometer and absorption photometer measurements. The nephelometer/absorption-photometer results were obtained on the ACE 2 ship (10 m asl), at the Sagres, Portugal site at 50 m asl, and also on the Pelican aircraft. This paper presents and compares the TARFOX and ACE 2 SSA results from the above techniques for different situations (e.g., marine vs continental flows, "clean" vs polluted conditions). It also discusses the strengths and limitations of the techniques, including whether they describe the aerosol in its ambient state or as perturbed by sampling processes; whether they describe the aerosol at the surface, as a function of altitude, or integrated over a column; the ease of acquiring representative data sets; results obtained in tests of consistency with radiative flux changes, and the likelihood of various artifacts and errors.

Russell, P. B.↗
NASA NTRS2001

Low-Pressure Long-Term Xenon Storage for Electric Propulsion

This Phase 2 effort demonstrated an alternative Xe storage and regulation system using activated carbon (AC) as a secondary storage media (ACSFR). This regulator system is nonmechanical, simple, inexpensive, and lighter. The ACSFR system isolates the thruster from the compressed gas tank, and allows independent multiple setpoint thruster operation. The flow using an ACSFR can also be throttled by applying increments in electrical power. Primary storage of Xe by AC is not superior to compressed gas storage with regard to weight, but AC storage can provide volume reduction, lower pressures in space, and potentially in situ Xe purification. With partial fill designs, a primary AC storage vessel for Xe could also eliminate problems with two-phase storage and regulate pressure. AC could also be utilized in long-term large quantity storage of Xe serving as a compact capture site for boil-off. Several Xe delivery ACSFR protocols between 2 and 45 sccm, and 15 min to 7 hr, were tested with an average flow variance of 1.2 percent, average power requirements of 5 W, and repeatability s of about 0.4 percent. Power requirements are affected by ACSFR bed sizing and flow rate/ duration design points, and these flow variances can be reduced by optimizing PID controller parameters.

Back, Dwight D.↗
NASA NTRS2004

Microgravity Testing of a Surface Sampling System for Sample Return from Small Solar System Bodies

The return of samples from solar system bodies is becoming an essential element of solar system exploration. The recent National Research Council Solar System Exploration Decadal Survey identified six sample return missions as high priority missions: South-Aitken Basin Sample Return, Comet Surface Sample Return, Comet Surface Sample Return-sample from selected surface sites, Asteroid Lander/Rover/Sample Return, Comet Nucleus Sample Return-cold samples from depth, and Mars Sample Return [1] and the NASA Roadmap also includes sample return missions [2] . Sample collection methods that have been flown on robotic spacecraft to date return subgram quantities, but many scientific issues (like bulk composition, particle size distributions, petrology, chronology) require tens to hundreds of grams of sample. Many complex sample collection devices have been proposed, however, small robotic missions require simplicity. We present here the results of experiments done with a simple but innovative collection system for sample return from small solar system bodies.

Franzen, M. A.↗
DOE OSTI2025

Chemical Composition and Mixing State of Wintertime Aerosol from the European Arctic Site of Ny-Ålesund, Svalbard

The Arctic is rapidly warming, and aerosols play an increasingly important role by scattering and absorbing sunlight and by participating in cloud formation. Their optical and cloud-forming properties depend on the mixing state and chemical composition, but observations of these features remain limited. This study comprehensively characterizes 25,254 individual particles collected at Ny-Ålesund, Svalbard (November −December 2020), using microspectroscopy techniques to investigate their size, morphology, mixing state, and chemical composition. Fresh sea salt aerosols (SSA) were identified as the most abundant (∼85%), of the total observed aerosol population, with potential sources from sea spray and blowing snow. Air masses originating from the Arctic Ocean surrounding Svalbard likely contribute to increased concentrations of sub-micrometer “Fresh SSA” particles. “Aged SSA” particles (7.4%) are enriched in sulfur and nitrogen, compared to “Fresh SSA”. These elevated ratios may result from various atmospheric aging processes including the uptake of sulfuric and nitric acids. Here, our results suggest that aged SSA, with sizes larger than 300 nm, likely underwent chlorine depletion by sulfuric and nitric acids during transport. Additionally, elemental analysis reveals that both fresh and aged SSA can mix with dust particles, regardless of the SSA size (49.9% in sub-micrometer size and 50.1% in super-micrometer size, respectively). Dust particles are efficient ice-nucleating particles (INPs), and SSA is known to act as cloud condensation nuclei (CCN), and therefore, their mixtures may inherit both properties. The non-negligible number (4.4%) of SSA-dust mixtures underscores the importance of these particles as potential sources of CCN and INP in the Arctic atmosphere.

Arctic↗
DOE OSTI2022

Orthoimagery and Shapefiles Documenting Pre- and Post-August 2019 Slope Disturbances, Teller Road Site, Seward Peninsula, Alaska, 2018-2019

This dataset was derived from UAS aerial photos and dGPS data collected at the Teller mile marker 47 site in 2018 and 2019 and used to support research quantifying the timing and rate of surface movements and analyze soil transport process in Arctic landscapes. In July 2018, a Phantom uncrewed aerial system (UAS) collected >6800 high resolution aerial photos of the lower portion of the Teller 47 watershed (see for raw photos; pending archive NGA281). During the UAS survey, 25 x 25 cm tile ground control points (GCPs) were laid out and secured with one rebar rod in the center. The four corners and rebar tops were surveyed with differential GPS, and these coordinates were used to construct and validate an orthomosaic of the site. These points were resurveyed in August 2019 and used to track annual movement. Changes in position between the two surveys are reported in (Lathrop et al. 2022; NGA254). Agisoft Metashape photogrammetry software was used to construct a georeferenced orthomosaic image (*.tif file) of a portion (0.68 km2) of the watershed with a final resolution of ~1 cm. Manual delineation of the perimeters of failures visible in the UAS imagery (*.tif files) was conducted to create shapefile polygons (two *.zip files). The failures were identified by the exposure of bare mineral soils, which were made visible by disruption of the overlying tundra vegetation. The shapefiles were then used to analyse the topographic distribution and sizes of the failures. In August 2019 an additional ~300 georeferenced UAS images of slope instability features were collected (data pending submission) and compared with the 2018 orthomosaic. Overview maps of the failure locations included as a *.pdf.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Additively manufactured Al-Ce-Ni-Mn alloy with improved elevated-temperature fatigue resistance

Here, the high cycle fatigue behavior of an additively manufactured (AM) Al-10.5Ce-3.1Ni-1.2Mn wt% alloy was evaluated at 350 °C. The measured fatigue strength of 50 MPa at this temperature is comparable to the most fatigue resistant wrought Al alloys (2618-T6 and 7079-T6) at 315 °C. Refinement of pore populations through advanced AM processing in the examined alloy led to oxide inclusions becoming dominant fatigue crack initiation sites. The distribution of microstructural features that determine crack initiation was measured by X-ray computed tomography and served as input to make fatigue strength model predictions with various methodologies. A Monte-Carlo based approach that was previously applied to predict the fatigue strength of cast aluminum alloys through pore size distributions yielded accurate predictions for the fatigue strength of this AM alloy. Given the tunability of defect distributions in AM alloys, the sensitivity of the Al-Ce-Ni-Mn alloy fatigue behavior to defect distributions and outstanding elevated-temperature fatigue resistance of this alloy; the results together suggest the possibility of a new generation of fatigue-resistant alloys produced by the additive manufacturing route.

36 MATERIALS SCIENCE↗
DOE OSTI2021

In situ transmission electron microscopy with dual ion beam irradiation and implantation

To study the helium effects and their interactions with displacement damage in irradiated materials, an in situ dual-ion beam irradiation capability with transmission electron microscopy was recently established at the IVEM-Tandem Facility at Argonne National Laboratory. Pure nickel was irradiated in situ individually with 1 MeV Kr ions for displacement damage study, 16 keV He ions for helium implantation, and simultaneously with 1 MeV Kr ions and 16 keV He ions at the rate of 1 at.% He/dpa to study the interaction of helium and displacement damage at 500 degrees C. Helium bubbles were formed and segregated within dislocation loops during the He implantation experiment and no bubbles were observed outside the loops. The loop size increased with increasing helium concentration. In contrast, helium bubbles were formed uniformly in the matrix when nickel was irradiated simultaneously with 1 MeV Kr ions and 16 keV He ions. Overall, it is suggested that the uniformly-distributed defect clusters formed under 1 MeV Kr ion irradiation serve as trapping sites of helium atoms resulting in homogeneous nucleation of helium bubbles under the dualion beam irradiation in nickel.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Directional clogging and phase separation for disk flow through periodic and diluted obstacle arrays

We model collective disk flow though a square array of obstacles as the flow direction is changed relative to the symmetry directions of the array. At lower disk densities there is no clogging for any driving direction, but as the disk density increases, the average disk velocity decreases and develops a drive angle dependence. For certain driving angles, the flow is reduced or drops to zero when the system forms a heterogeneous clogged state consisting of high density clogged regions coexisting with empty regions. The clogged states are fragile and can be unclogged by changing the driving angle. For large obstacle sizes, we find a uniform clogged state that is distinct from the collective clogging regime. Within the clogged phases, depinning transitions can occur as a function of increasing driving force, with intermittent motion appearing just above the depinning threshold. The clogging is robust against the random removal or dilution of the obstacle sites, and the disks are able to form system-spanning clogged clusters even under increasing dilution. If the dilution becomes too large, however, the clogging behavior is lost.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo

Abstract Proper development depends on precise spatiotemporal gene expression patterns. Most developmental genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical “sharp” developmental promoter, while the other resembles a “broad” promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter, indicating that promoters provide both redundancy and specificity. By analyzing the reporter dynamics, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the combination of promoter and enhancer. Using locus-sized reporters, we discovered that enhancers with no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is due both to enhancer preference and a need for redundancy and that “broad” promoters with dispersed transcription start sites are common among developmental genes. They also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where other variables shape a gene’s overall expression pattern.

Li, Lily (ORCID:0000000301986521)↗
DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗