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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Single cell RNA sequencing reveals shifts in cell maturity and function of endogenous and infiltrating cell types in response to acute intervertebral disc injury

Intervertebral disc (IVD) degeneration contributes to disabling back pain. Degeneration can be initiated by injury and progressively leads to an irreversible loss of cells and function. IVD function restoration through cell replacement therapies have had limited success due to knowledge gaps in the critical cell populations important for repair. Here, in this study, we used single cell RNA sequencing to identify the transcriptional changes of IVD resident and infiltrating cell populations from Control and Injured coccygeal IVDs extracted from 12-week-old female C57BL/6J mice 7 days post injury. Clustering, gene ontology, and pseudotime trajectory analyses determined transcriptomic divergences with injury, flow cytometry identified they types of infiltrating immune cells, and immunofluorescence was utilized to define mesenchymal stem cell (MSC) localization. We identified 11 distinct clusters that included IVD, immune, vascular cells, and MSCs. Differential gene expression analysis determined that Outer Annulus Fibrosus, Neutrophils, Saa2-High MSCs, Macrophages, and Krt18 + Nucleus Pulposus (NP) cells were the major drivers of transcriptomic differences between Control and Injured cells. Gene ontology revealed that the most upregulated biological pathways were angiogenesis and T cell-related while wound healing and ECM regulation were downregulated. Pseudotime trajectory analyses revealed that IVD injury directed cells towards increased differentiation in all clusters, except for Krt18 + NP cells which remained in a less mature cell state. Saa2-High and Grem1-High MSCs populations shifted towards more differentiated IVD cells profiles with injury and localized distinctly within the IVD. This study revealed novel MSC populations with the potential to be leveraged for future IVD repair studies.

Cartilage↗
DOE OSTI2025

Landscaper v1

Understanding the inner workings of machine learning models through their loss landscapes offers crucial insights into model properties, optimization dynamics, and generalizability. However, accessing these insights has traditionally required specialized mathematical expertise, limiting broader adoption. Landscaper is an open-source Python package designed to bridge this gap. Landscaper seamlessly integrates a suite of multi-dimensional loss landscape analyses with cutting-edge topological data analysis (TDA) methods. This powerful combination makes both fundamental loss landscape analysis and advanced TDA techniques accessible to the broader scientific ML community, without requiring deep pre-existing mathematical knowledge. Landscaper offers three key functionalities: * Construction: Builds detailed loss landscape representations through versatile low and high-dimensional sampling techniques. * Quantification: Applies advanced metrics, including a novel topological data analysis (TDA) based smoothness metric, enabling new perspectives on model behavior. * Visualization: Offers intuitive tools to visualize and interpret loss landscapes, providing actionable insights beyond traditional performance metrics.

Weber, Gunther [Lawrence Berkeley National Laborat↗
DOE OSTI2025

Characterization of Gramicidin A in Triblock and Diblock Polymersomes and Hybrid Vesicles via Continuous Wave Electron Paramagnetic Resonance Spectroscopy

Studying membrane proteins in a native environment is crucial to understanding their structural and/or functional studies. Often, widely accepted mimetic systems have limitations that prevent the study of some membrane proteins. Micelles, bicelles, and liposomes are common biomimetic systems but have problems with membrane compatibility, limited lipid composition, and heterogeneity. To overcome these limitations, polymersomes and hybrid vesicles have become popular alternatives. Polymersomes form from amphiphilic triblock or diblock copolymers and are considered more robust than liposomes. Hybrid vesicles are a combination of lipids and block copolymers that form vesicles composed of a mixture of the two. These hybrid vesicles are appealing because they have the native lipid environment of bilayers but also the stability and customizability of polymersomes. Gramicidin A was incorporated into these polymersomes and characterized using continuous wave electron paramagnetic resonance (CW-EPR) and transmission electron microscopy (TEM). EPR spectroscopy is a powerful biophysical technique used to study the structure and dynamic properties of membrane proteins in their native environment. Spectroscopic studies of gramicidin A have been limited to liposomes; in this study, the membrane peptide is studied in both polymersomes and hybrid vesicles using CW-EPR spectroscopy. Lineshape analysis of spin-labeled gramicidin A revealed linewidth broadening, suggesting that the thicker polymersome membranes restrict the motion of the spin label more when compared to liposome membranes. Statement of Significance: Understanding membrane proteins’ structures and functions is critical in the study of many diseases. In order to study them in a native environment, membrane mimetics must be developed that can be suitable for obtaining superior biophysical data quality to characterize structural dynamics while maintaining their native functions and structures. Many currently widely accepted methods have limitations, such as a loss of native structure and function, heterogeneous vesicle formation, restricted lipid types for the vesicle formation for many proteins, and experimental artifacts, which leaves rooms for the development of new biomembrane mimetics. The triblock and diblock polymersomes and hybrid versicles utilized in this study may overcome these limitations and provide the stability and customizability of polymersomes, keeping the biocompatibility and functionality of liposomes for EPR studies of membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Wafer-scale waveguide sidewall roughness scattering loss characterization by image processing

Photonic integrated circuits (PICs) are vital for developing affordable, high-performance optoelectronic devices that can be manufactured at an industrial scale, driving innovation and efficiency in various applications. Optical loss of modes in thin film waveguides and devices is a critical measure of their performance. Thin film growth, lithography, masking, and etching processes are imperfect processes that introduce significant sidewall and top-surface roughness and cause dominating optical losses in waveguides and photonic structures. This roughness, as perturbations couple light from guided to far-field radiation modes, leads to scattering losses that can be estimated from theoretical models. Typically, with UV-based lithography, sidewall roughness is significantly larger than wafer-top surface roughness. Atomic force microscopy (AFM) imaging measurement gives a 3D and high-resolution roughness profile, but the measurement is inconvenient, costly, and unscalable for large-scale PICs and at wafer-scale. Here, we evaluate the sidewall roughness profile based on 2D high-resolution scanning electron microscope (SEM) imaging. We characterized the loss on two homemade nitride and oxide films on 3-inch silicon wafers with 12 waveguide devices on each and correlated the scattering loss estimated from a 2D image-based sidewall profile and theoretical Payne model. The lowest loss of guided fundamental transverse electric (TE 0 ) mode is found at 0.075 dB/cm at 633 nm across 24 devices, a record at visible wavelength. Our work shows 100% success (edge continuity span exceeding 95% of image width/height) in edge detection in image processing of all images to estimate autocorrelation function and optical mode loss. These demonstrations offer valuable insights into waveguide sidewall roughness and a comparison of experimental and 2D SEM image processing based loss estimations with applications in loss characterization at wafer-scale PICs.

Khurana, Mohit (ORCID:0000000207898672)↗
DOE OSTI2025

Electrocatalytic grafting of polyvinyl chloride plastics

Polyvinyl chloride (PVC) plastics require high loadings of plasticizers and stabilizers to achieve commercially useful bulk properties. However, these non-covalent additives leach from PVC over time, resulting in the loss of their tailored functionality. This work details the electrocatalytic functionalization of PVC to covalently graft plasticizing additives directly onto the polymer backbone. Here, mechanistic insights guided the design of electrocatalysts capable of modifying C–Cl bonds of PVC under mild conditions with high selectivity while suppressing side reactions such as elimination and chain scission. Functional groups that mimic PVC plasticizers are covalently installed into the backbone of PVC to create new materials with distinct bulk properties from the original polymer. The degree of polymer grafting is easily controlled by simply changing the redox capacity that is passed during electrolysis. This strategy is employed to create chemically- and leach-resistant PVC materials by directly electrolyzing mixtures of consumer PVC products

Zackasee, Jordan L.S.↗
DOE OSTI2024

Triplet Management at Ligand-Perovskite Interface to Enhanced Photovoltaics Performance

Aromatic organic molecules are widely used as passivators in perovskite solar cells (PSCs). Efforts have been devoted to improving the energy alignments, band edge states, and defect passivation functionalities. However, potential energy loss through triplet states in such conjugated molecules has not been investigated in the past. Here, we report the observation of charge transfer from FAPbI 3 to the triplet state of a pyrene (Pyr)-based cationic ligand. Such a potential loss channel can be suppressed via delicate triplet management in polycyclic aromatic compounds. Interestingly, a subtle structural modification from Pyr to the triphenylene (TP) core gave rise to shallower triplets that prohibit electron transfer from perovskites. This strategy has led to TP-passivated PSCs achieving an enhanced power conversion efficiency (PCE) of 24.69% from 23.10% in Pyr-passivated counterparts. Moreover, the devices retained above 80% initial PCE after 4000 h of light soaking, which likely benefited from the reduced triplet electron trapping at the ligand-perovskite interface.

14 SOLAR ENERGY↗
DOE OSTI2026

SPRUCE FT-ICR MS, Bulk Chemistry, and Mass Loss from Litter Decomposition Study in Experimental Plots, Marcell Experimental Forest, Minnesota, 2015-2017

This dataset contains molecular, bulk chemical, and mass loss measurements from a litter decomposition study at the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental site within the Marcell Experimental Forest in northern Minnesota, USA. This site is in a Sphagnum spp. ombrotrophic bog forest. Litterbags were deployed into the peat in September 2015 across three warming levels (+0, +4.5, and +9°C) under ambient and elevated carbon dioxide (CO₂ - +500 ppm) and retrieved after roughly 0.5, 1, and 2 years of field incubation (2015-09-23 to 2017-08-02). Litterbags containing six peatland litter types: black spruce needles (Picea mariana - SPL), spruce fine roots (SPR), Sphagnum angustifolium (ANG), Sphagnum magellanicum (MAG), Labrador tea leaves (Rhododendron groenlandicum - LTL), and Labrador tea roots (LTR). Molecular composition of water-soluble organic matter extracts was characterized using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) at 9.4 Tesla, operated in negative ion mode with electrospray ionization, providing molecular formula assignments and compound-class distributions across the decomposition time series. Bulk chemical characterization included elemental analysis (percent carbon, nitrogen, and phosphorus) and Fourier Transform Infrared Spectroscopy (FTIR) to quantify functional group composition. Litter mass loss was tracked gravimetrically at each retrieval interval, expressed as percent mass remaining relative to initial dry mass for each litter type and treatment combination. These data are valuable for understanding how vegetation shifts driven by increased atmospheric CO2 and temperature in peatlands alter litter inputs and organic matter stabilization trajectories, with implications for projecting and modeling peatland carbon cycling. This dataset contains two data files in comma-separated value (.csv) format. Additional metadata are provided: two data dictionaries and a file-level metadata file in comma separate (.csv) format and a user guide in PDF (*.pdf) format.

decomposition↗
DOE OSTI2025

Likelihood-Based Particle Identification in the Short-Baseline Near Detector

Accurate particle identification is crucial in any high-energy physics experiment, allowing scientists to understand the unique interactions and mechanisms at play in a detector. In this project, I develop and study a new particle identification (PID) algorithm for the Short-Baseline Near Detector, a likelihood-based approach, different from out current $\chi^2$ method. A likelihood estimation offers a more physically motivated strategy for PID. The distribution random energy losses of charged particles traveling through a medium are described by the Vavilov probability density function. By using this model, we can account for random energy losses and construct likelihood functions specific to each particle type, potentially enabling a more accurate method for PID.

Vanderwaal, Sophia [U. Alabama, Huntsville] (ORCID↗
DOE OSTI2024

Dielectric and magnetic properties of microwave-absorbing FeAl x O y catalysts fabricated via solution combustion synthesis

Iron-based alumina (FeAl x O y ) nanocomposites are microwave-absorbers and catalysts, which makes them promising for emerging microwave-assisted thermocatalytic technologies. Solution combustion synthesis (SCS) has been used to synthesize FeAl x O y powders, and prior work has demonstrated that adjusting SCS parameters significantly changes phase composition and specific surface area of the products. However, it is unclear how synthesis parameters affect their microwave-absorbing properties, which are essential for optimizing microwave-assisted technologies. To address this challenge, in the present work, twelve different FeAl x O y products were synthesized at different combinations of the SCS parameters such as two fuels (citric acid and glycine), two heating modes (hotplate and muffle furnace), and three Fe:Al molar ratios (2:1, 1:1, 1:2). Dielectric and magnetic properties of the products were characterized using a network analyzer and a vibrating sample magnetometer. Based on the measured permittivity and permeability, penetration depth and reflection loss were calculated as a function of frequency and bed thickness. The products were heated by microwaves at 2.45 GHz and then examined with X-ray diffraction (XRD) analysis. For all products, the magnetic saturation was lower than for bulk iron oxides because of the small crystallite size and aluminum substitution. The use of glycine induced high dielectric losses and enabled fast microwave-heating rates compared to citric acid. Higher Fe:Al ratio also led to higher dielectric and magnetic losses. With glycine fuel, SCS in a furnace induced larger penetration depth and lower microwave absorption than SCS on a hotplate. The minimization of reflected power was more sensitive to the thickness of the product bed than to the frequency of the electromagnetic field. Post-heating XRD analysis revealed different phase transformations in the FeAl x O y powders depending on the SCS parameters. As a result, an FeAl x O y material, synthesized via incipient wetness impregnation, lacked magnetic losses and did not heat well as compared to the SCS products.

Combustion synthesis↗
DOE OSTI2025

Two-Dimensional Siloxene Nanosheets: Understanding the Effect of Heat Treatment on the Surface Chemistry and Resulting Electrochemistry in Lithium-Based Batteries

Two-dimensional (2D) silicon materials are conceptually appealing as negative electrode materials in lithium-ion batteries due to their layered morphology, which can accommodate (de)lithiation-induced volume changes. Herein, heat treatment of 2D Siloxene materials was used to modify the surface functional groups to determine the impact on the electrochemical behavior. Spectroscopic characterization of the heat-treated nanosheets confirmed the loss of oxygenated and hydride surface functional groups with an increased annealing temperature. Formation and disproportionation of the amorphous suboxides with increasing heat treatment were affirmed with lab and synchrotron-based measurements. A reduced irreversible capacity was observed for Siloxene with a higher temperature heat treatment consistent with the formation of a more favorable surface electrolyte interphase (SEI). A Siloxene-400||NMC622 full cell (prepared with 400 °C-annealed Siloxene (Siloxene-400) and LiNi 0.6 Mn 0.2 Co 0.2 O 2 (NMC622)) showed significantly enhanced capacity and rate capability compared to a nano Si||NMC622 cell. Finally, these results illustrate the ability of thermal annealing to modify the surface functional groups of Siloxene and highlight the favorable impact of the appropriate surface functionality on the electrochemistry of Siloxene in lithium cells.

25 ENERGY STORAGE↗
DOE OSTI2024

Bottomonium suppression in 5.02 and 8.16 TeV 𝑝-Pb collisions

Here, we compute the suppression of ϒ⁡(1⁢𝑆), ϒ⁡(2⁢𝑆), and ϒ⁡(3⁢𝑆) states in 𝑝-Pb collisions relative to 𝑝⁢𝑝 collisions, including nuclear parton distribution function (nPDF) effects, coherent energy loss, momentum broadening, and final-state interactions in the quark-gluon plasma. We employ the EPPS21 nPDFs and calculate the uncertainty resulting from variation over the associated error sets. To compute coherent energy loss and momentum broadening, we follow the approach of Arleo, Peigne, and collaborators. The 3+1⁢D viscous hydrodynamical background evolution of the quark-gluon plasma is generated by anisotropic hydrodynamics. The in-medium suppression of bottomonium in the quark-gluon plasma is computed using a next-to-leading-order open quantum system framework formulated within potential nonrelativistic quantum chromodynamics. We find that inclusion of all these effects provides a reasonable description of experimental data from the ALICE, ATLAS, CMS, and LHCb Collaborations for the suppression of ϒ⁡(1⁢𝑆), ϒ⁡(2⁢𝑆), and ϒ⁡(3⁢𝑆) as a function of both transverse momentum and rapidity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Enhanced Monte Carlo Simulations for Electron Energy Loss Mitigation in Real-Space Nanoimaging of Thick Biological Samples and Microchips

High-resolution imaging using Transmission Electron Microscopy (TEM) is essential for applications such as grain boundary analysis, microchip defect characterization, and biological imaging. However, TEM images are often compromised by electron energy spread and other factors. In TEM mode, where the objective and projector lenses are positioned downstream of the sample, electron–sample interactions cause energy loss, which adversely impacts image quality and resolution. This study introduces a simulation tool to estimate the electron energy loss spectrum (EELS) as a function of sample thickness, covering electron beam energies from 300 keV to 3 MeV. Leveraging recent advances in MeV-TEM/STEM technology, which includes a state-of-the-art electron source with 2-picometer emittance, an energy spread of 3 × 10 -5 , and optimized beam characteristics, we aim to minimize energy spread. By integrating EELS capabilities into the BNL Monte Carlo (MC) simulation code for thicker samples, we evaluate electron beam parameters to mitigate energy spread resulting from electron–sample interactions. Based on our simulations, we propose an experimental procedure for quantitively distinguishing between elastic and inelastic scattering. The findings will guide the selection of optimal beam settings, thereby enhancing resolution for nanoimaging of thick biological samples and microchips.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Astrocyte Reactivity by Alcohol Dependence in the Central Amygdala

Astrocytes play essential roles in the brain, but prolonged insult can result in the loss or diminishment of homeostatic functions and increased neuroinflammatory response. The central amygdala (CeA) is an important limbic region in reward and stress responsivity as well as in the development of alcohol dependence. Using a multi-omics approach with Aldh1l1-EGFP/Rpl10a mice and the chronic intermittent ethanol – two-bottle choice exposure model, we have characterized the translational response of CeA astrocytes, as well as the proteomic and phosphoproteomic changes in dependent, non-dependent, and naïve mice. We identified astrocyte-specific alterations in neuroimmune functions and antioxidant/oxidative stress pathways in dependent animals while non-dependent EtOH drinking altered cytoskeletal plasticity related pathways. Proteomic analysis showed down-regulation of astrocyte physiological functions in dependent animals while phosphoproteomic analysis identified cytoskeleton remodeling in both dependent and non-dependent animals suggesting the development of a reactive astrocyte phenotype. Astrocyte morphological reconstruction showed increased CeA astrocyte complexity in dependent and non-dependent groups compared to naïve mice. The astrocyte-specific increase in neuroimmune functions, down-regulation of astrocyte homeostatic functions, alteration in protein phosphorylation-mediated cytoskeleton remodeling, and increased astrocyte complexity demonstrate EtOH induced astrocyte activation in the CeA and suggest the presence of both adaptive and maladaptive reactive astrocytes. These findings highlight the roles CeA astrocytes play in the progression of alcohol intake to dependence and are the first step in the identification of novel astrocyte-specific therapeutic approaches for alcohol use disorder through the potentiation of adaptive changes and inhibition of maladaptive changes in astrocytes.

Hashimoto, Joel↗
DOE OSTI2024

Suppressed deprotonation enables a durable buried interface in tin-lead perovskite for all-perovskite tandem solar cells

Low-band-gap tin (Sn)-lead (Pb) perovskites are a critical component in all-perovskite tandem solar cells (APTSCs). Current state-of-the-art Sn-Pb perovskite devices exclusively use poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) as the hole-transport layer (HTL) but suffer from undesired buried-interface degradation. Here, we show that the deprotonation of the –SO 3 H group in PSS is the root cause of the interface degradation due to its low acid dissociation constant (pK a ), leading to acidic erosion and iodine volatilization in Sn-Pb perovskites. We identify that HTL featuring the carboxyl (–COOH) group with a higher pK a , such as poly[3-(4-carboxybutyl)thiophene-2,5-diyl] (P3CT), can suppress deprotonation and strengthen the interface, mitigating the buried-interface degradation. Motivated by established P3CT modification, we introduce Pb doping to P3CT to increase its work function and reduce interfacial energy loss. Furthermore, we fabricate APTSCs with a champion efficiency of 27.8% and an operational lifetime of over 1,000 h, with 97% retaining efficiency under maximum power point tracking.

08 HYDROGEN↗
DOE OSTI2024

DiffLense: a conditional diffusion model for super-resolution of gravitational lensing data

Abstract Gravitational lensing data is frequently collected at low resolution due to instrumental limitations and observing conditions. Machine learning-based super-resolution techniques offer a method to enhance the resolution of these images, enabling more precise measurements of lensing effects and a better understanding of the matter distribution in the lensing system. This enhancement can significantly improve our knowledge of the distribution of mass within the lensing galaxy and its environment, as well as the properties of the background source being lensed. Traditional super-resolution techniques typically learn a mapping function from lower-resolution to higher-resolution samples. However, these methods are often constrained by their dependence on optimizing a fixed distance function, which can result in the loss of intricate details crucial for astrophysical analysis. In this work, we introduce DiffLense , a novel super-resolution pipeline based on a conditional diffusion model specifically designed to enhance the resolution of gravitational lensing images obtained from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). Our approach adopts a generative model, leveraging the detailed structural information present in Hubble space telescope (HST) counterparts. The diffusion model, trained to generate HST data, is conditioned on HSC data pre-processed with denoising techniques and thresholding to significantly reduce noise and background interference. This process leads to a more distinct and less overlapping conditional distribution during the model’s training phase. We demonstrate that DiffLense outperforms existing state-of-the-art single-image super-resolution techniques, particularly in retaining the fine details necessary for astrophysical analyses.

Computer Science↗
DOE OSTI2025

Metalens formed by structured arrays of atomic emitters

Abstract Arrays of atomic emitters have proven to be a promising platform to manipulate and engineer optical properties, due to their efficient cooperative response to near‐resonant light. Here, we theoretically investigate their use as an efficient metalens. We show that, by spatially tailoring the (subwavelength) lattice constants of three consecutive two‐dimensional arrays of identical atomic emitters, one can realize a large transmission coefficient with arbitrary position‐dependent phase shift, whose robustness against losses is enhanced by the collective response. To characterize the efficiency of this atomic metalens, we perform large‐scale numerical simulations involving a substantial number of atoms (N∼ 5 × 10 5 ) that is considerably larger than comparable works. Our results suggest that low‐loss, robust optical devices with complex functionalities, ranging from metasurfaces to computer‐generated holograms, could be potentially assembled from properly engineered arrays of atomic emitters.

Materials Science↗
DOE OSTI2026

Cellular signaling within aged skeletal muscle reveals a dysregulated stress-induced remodeling response following volumetric muscle loss in female mice

Severe muscle trauma disrupts endogenous repair mechanisms, producing chronic functional deficits that are incompletely characterized in aged populations. This study investigated inflammatory, molecular, and physiological responses to volumetric muscle loss in young adult and aged female mice. Serum cytokine profiling revealed elevated baseline inflammation in aged animals and a blunted response to injury, with cytokines such as IL-6 increasing 4.4-fold in young versus 1.8-fold in aged mice at day 3 compared to baseline. By day 28 post-injury, histological analyses showed comparable reductions in muscle size and increases in fibrosis across ages. Despite these similar tissue-level outcomes, age-dependent differences emerged in downstream functional and molecular responses. Muscle functional testing demonstrated persistent force deficits independent of age but altered muscle relaxation kinetics in aged mouse muscles (p < 0.001), suggesting dysregulated excitation-contraction coupling. Additionally, mice displayed age-associated differences in post-injury limb loading. Global proteomic analyses further confirmed age-associated enrichment of complement and antigen-processing pathways alongside metabolic dysfunction (p < 0.05). Phosphoproteomic profiling revealed reduced basal kinase activity in the muscles of aged mice yet exaggerated injury-induced phosphorylation of Mapk1-associated phosphosites, indicating a dysregulated stress response. Collectively, these findings suggest that aged murine muscles function within a heightened inflammatory and perturbed kinase-signaling environment that may hinder the coordination of regenerative programs, underscoring the need for regenerative strategies that address age-specific molecular contexts to improve functional recovery across the lifespan.

Habing, Krista M.↗
DOE OSTI2025

In vivo mapping of mutagenesis sensitivity of human enhancers

Distant-acting enhancers are central to human development1. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease2. Here we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers that are active in the developing brain, heart, limb and face, we created over 1,700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-base-pair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modelling, we annotated critical nucleotides at the base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes in in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features that are required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.

Kosicki, Michael↗