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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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49 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Integrating N -glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung

Identifying cell-specific glycan structures in human lungs is critical for understanding the chemistry and mechanisms that guide cell–cell and cell–matrix interactions and determining nuanced functions of specific glycosylation. Our dual-modality omics platform, which uses matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to profile glycan chemistry at 50 μm × 50 μm scale, combined with co-detection by indexing (CODEX) to provide cell identification from the exact same tissue section, is a significant step in this direction. It enabled us to detect, differentiate, and reveal chemical properties of N-glycans in the various cell types of a human lung, suggesting the cell-specific function of distinct carbohydrate moieties. This innovative technological combination bridges the gap between the specific protein glycosylation and their cellular origin, paving the way for targeted studies in the lungs and many other human tissues where glycans mediate cell–cell recognition events.

Veličković, Dušan [Pacific Northwest National Labo↗
DOE OSTI2024

X-ray fluorescence mapping of brain tissue reveals the profound extent of trace element dysregulation in stroke pathophysiology

Abstract The brain is a privileged organ with regard to its trace element composition and maintains a robust barrier system to sequester this specialized environment from the rest of the body and the vascular system. Stroke is caused by loss of adequate blood flow to a region of the brain. Without adequate blood flow ischaemic changes begin almost immediately, triggering an ischaemic cascade, characterized by ion dysregulation, loss of function, oxidative damage, cellular degradation, and breakdown of the barrier that helps maintain this environment. Ion dysregulation is a hallmark of stroke pathophysiology and we observe that most elements in the brain are dysregulated after stroke. X-ray fluorescence-based detection of physiological changes in the neurometallome after stroke reveals profound ion dysregulation within the lesion and surrounding tissue. Not only are most elements significantly dysregulated after stroke, but the level of dysregulation cannot be predicted from a cell-level description of dysregulation. X-ray fluorescence imaging reveals that the stroke lesion retains <25% of essential K+ after stroke, but this element is not concomitantly elevated elsewhere in the organ. Moreover, elements like Na+, Ca2+, and Cl− are vastly elevated above levels available in normal brain tissue (>400%, >200%, and >150%, respectively). We hypothesize that weakening of the blood–brain barrier after stroke allows elements to freely diffuse down their concentration gradient so that the stroke lesion is in equilibrium with blood (and the compartments containing brain interstitial fluid and cerebrospinal fluid). The change observed for the neurometallome likely has consequences for the potential to rescue infarcted tissue, but also presents specific targets for treatment.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Unraveling the Dynamics of Nucleosome Arrays

The organization of genomic DNA into chromatin is a fundamental determinant of genome stability, regulation, and cellular function. Nucleosomes, the basic repeating units of chromatin, assemble into higher-order structures whose organization and heterogeneity remain difficult to characterize using conventional ensemble-averaged techniques. A key need in the field is the development of experimental approaches capable of directly visualizing nucleosome assemblies and their structural variability at the single-molecule level. This LDRD Lab-Wide project focused on establishing and evaluating atomic force microscopy (AFM)–based approaches for the characterization of nucleosome assemblies. The work emphasized experimental workflows for preparing, imaging, and assessing multi-nucleosome systems, rather than isolated single nucleosomes. Through method development and exploratory measurements, the project demonstrated the feasibility of applying scanning probe microscopy to investigate chromatin-relevant assemblies and provided preliminary insight into the strengths and limitations of this approach for future quantitative studies. Results and lessons learned from this effort were disseminated to the broader scientific community through multiple national conference presentations, helping to position LLNL for continued work in chromatin and genome organization research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Electron microscopy evidence of gadolinium toxicity being mediated through cytoplasmic membrane dysregulation

Past functional toxicogenomic studies have indicated that genes relevant to membrane lipid synthesis are important for tolerance to the lanthanides. Moreover, previously reported imaging of patient's brains following administration of gadolinium-based contrast agents shows gadolinium lining the vessels of the brain. Taken together, these findings suggest the disruption of cytoplasmic membrane integrity as a mechanism by which lanthanides induce cytotoxicity. In the presented work we used scanning transmission electron microscopy and spatially resolved elemental spectroscopy to image the morphology and composition of gadolinium, europium, and samarium precipitates that formed on the outside of yeast cell membranes. In no sample did we find that the lanthanide contaminant had crossed the cell membrane, even in experiments using yeast mutants with disrupted genes for sphingolipid synthesis—the primary lipids found in yeast cytoplasmic membranes. Rather, we have evidence that lanthanides are co-located with phosphorus outside the yeast cells. Finally, these results lead us to hypothesize that the lanthanides scavenge or otherwise form complexes with phosphorus from the sphingophospholipid head groups in the cellular membrane, thereby compromising the structure or function of the membrane, and gaining the ability to disrupt membrane function without entering the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Spatial Distribution and Clustering of Glycosaminoglycans in Electrospun Gelatin-Based Scaffolds

The extracellular matrix (ECM) is comprised of components like collagen, elastin, and glycosaminoglycans (GAGs). Electrospun fibrous scaffolds are designed to replicate the form and composition of the native ECM, often requiring blending of various ECM component mimics to enhance cellular responses. However, the spatial distribution of blended components within these fibers remains unclear. This study investigates the spatial distribution of chondroitin sulfate-C (CSC) in electrospun gelatin-based scaffolds. scanning electron microscopy (SEM), attenuated reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and Time-of-flight Secondary Ion Mass Spectrometry (ToF-SIMS) were applied for surface and subsurface chemical characterization of the fibrous scaffolds. SEM confirmed a fibrous morphology, while ATR-FTIR and XPS analyses indicated the presence of CSC through the identification of sulfate groups. ToF-SIMS imaging, alongside K-means clustering and Ripley’s K function, revealed a nonuniform CSC distribution with higher concentrations at the top layer of the scaffold. This study demonstrates that CSC presentation at the fiber surface varies with depth and differs from bulk incorporation while reveals nanoscale clustering and spatial heterogeneity at both the surface and subsurface of electrospun gelatin fibers. These findings define an underexplored design consideration with potential to influence cell–scaffold interactions.

Animal derived food↗
DOE OSTI2025

Generative diffusion model surrogates for mechanistic agent-based biological models

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models (DDPMs) to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Exploring strain rate effects upon 3D materials using high speed in situ X-ray tomoscopy

Cellular materials are ubiquitous in our modern society. They may be stochastic gas-blown foams (e.g., polyurethane), foamed starches (e.g., cereals), or, in this case, 3D printed microlattices. Failure in these materials is often driven by surface or sub-surface defects, which may be nucleated at a surface roughness, an interior void, or inclusion interfaces that may not be typically observable. Obfuscating our understanding further, bulk materials are known to exhibit strain-rate-dependent mechanical response, making a subsurface understanding of damage even more critical. For the first time, an in situ uniaxial mechanical loading stage that simultaneously rotates specimens up to 18 Hz was fielded at a synchrotron for 3D tomographic imaging. This capability opens a plethora of materials science opportunities to explore strain rate effects in materials and examining deformation, fracture, and delamination’s (in composites) for a complete 3D picture (movie) of material response. We demonstrate the deformation of 3D printed polymer lattice structures, of three different material types, at 0.25, 1.1, and 2.2 s −1 strain rates. We successfully imaged the 3D deformation of these materials and can directly compare the same printed structure to the three material types at three strain rates, all in 3D. Material point method simulations were applied to one of the materials to better understand the role of voids on the 3D printed structure’s performance.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Imaging and speciation of intracellular metallic implant debris using synchrotron-based X-ray fluorescence micro-spectroscopy: a study of two cases

Debris generated from total hip arthroplasty (THA) components made from metal alloys can cause, in some cases, inflammatory cell (e.g., macrophages) responses that lead to adverse local tissue reactions (ALTR) and implant failure. The lack of information on intracellular chemical alterations of metal debris has hindered the understanding of the pathogenesis of ALTR. The goal of this study was to characterize intracellular debris within macrophages using Synchrotron imaging and spectroscopy. We studied periprosthetic tissues of two retrieved THAs with (1) a metal-on-metal (MoM) articulation and (2) a metal-on-polyethylene (MoP) articulation exhibiting corrosion of the metal femoral head. The MoM-THA exhibited different valence states of chromium- and cobalt-containing debris, suggesting three different moieties: Cr 2 O 3 , CrPO 4 , and an alloy-oxide mixture. The findings further suggest that Cr 2 O 3 formed in the tribological interfaces of the implant, while CrPO 4 is a by-product of the phagocytosis process of cobalt alloy-containing debris. Titanium debris appeared to occur in a mixed crystalline/amorphous oxide state. It remains unclear if this chemical state results from the tribochemical processes at the implant surface or intracellular alterations. The MoP-THA specimen exhibited no intracellular particulate debris associated with macrohpages, indicating that the ALTR may be entirely triggered by metal ionic species in this case. A better understanding of in vivo chemical alteration of implant debris will aid in assessing the risk for ALTR during implant design and material choice. However, various techniques are needed to accurately determine the interaction between metal particles and the inta- and extra-cellular environment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Cooperative Automated Cohort Driving on Connected Infrastructure, Arterial Roadways, and Highways: Final Project Demonstration and System-of-Systems Model Correlation

This project seeks to synergize vehicle automated driving and connectivity data to improve mobility and energy efficiency of groups of mixed vehicles operating in close proximity (vehicle cohort) on various infrastructure. A custom cellular communication network links vehicles operating as a cohort with infrastructure to a centralized system-of-systems digital twin with an AI-based optimal behavior planner. The data contained in this set are from final testing and technology demonstrations to U.S. Department of Energy staff at the American Center for Mobility. The data contain single-lane, single-light scenarios; multi-lane, multi-light arterial scenarios; and limited-access highway scenarios. All test cases were derived from simulations and replicated on the test track. The project employed two and four light-duty vehicles with connectivity and drive automation for the testing. The baseline scenario without connectivity was run under the control of the system-of-systems centralized planner but operating each vehicle with an intelligent driver model controlling the velocity, lane utilization, and vehicle gap. This was to ensure the highest compatibility with the simulation in terms of dynamic behavior. The connected cohort case utilized AI optimization to perform coordinated and cooperative control for energy, as well as safe, comfortable behavior for the cohort. The dataset is appropriately named with unconnected and connected designations, with comparisons sharing the same run index number. The included PowerPoint and PDF files describe the test setup and provide an overview of results from the project. ![image](de-EE0009209_March_2023_Data_Arterial_Scenario_Results.png)

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular “reactors.” In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Optical interference for the guidance of cryogenic focused ion beam milling beyond the axial diffraction limit

Cryogenic focused ion beam (Cryo-FIB) milling has become a standard step in the cryogenic electron tomography (Cryo-ET) workflow and is required to thin cells to electron-semitransparency. However, this destructive process removes the vast majority of the cellular material and raises a critical question: what thin section should be preserved for Cryo-ET analysis? Using a tri-coincident cryogenic FIB-SEM-LM system, we identify an interferometric optical response that can be used for targeting lamella production to fluorescently labeled structures with accuracy beyond the diffraction limit. Here we demonstrate this approach using synthetic samples of fluorescent beads embedded in micron-scale droplets of amorphous ice. We then apply the approach to capture virions inside host cells. Successful targeting is confirmed by Cryo-ET revealing clusters of virions in intracellular vesicles. The method does not require any fluorescent fiducials or axial registration and can be performed on any fluorescently labeled structure that is visible in widefield fluorescence microscopy.

Cryoelectron microscopy↗
DOE OSTI2024

In situ detection of ferric reductase activity in the intestinal lumen of an insect

The rise of atmospheric oxygen as a result of photosynthesis in cyanobacteria and chloroplasts has transformed most environmental iron into the ferric state. In contrast, cells within organisms maintain a reducing internal milieu and utilize predominantly ferrous iron. Ferric reductases are enzymes that transfer electrons to ferric ions, either extracellularly or within endocytic vesicles, enabling cellular ferrous iron uptake through Divalent Metal Transporter 1. In mammals, duodenal cytochrome b is a ferric reductase of the intestinal epithelium, but how insects reduce and absorb dietary iron remains unknown. Here we provide indirect evidence of extracellular ferric reductase activity in a small subset of Drosophila melanogaster intestinal epithelial cells, positioned at the neck of the midgut’s anterior region. Dietary-supplemented bathophenanthroline sulphate (BPS) captures locally generated ferrous iron and precipitates into pink granules, whose chemical identity was probed combining in situ X-ray absorption near edge structure and electron paramagnetic resonance spectroscopies. An increased presence of manganese ions upon BPS feeding was also found. Control animals were fed with ferric ammonium citrate, which is accumulated into ferritin iron in distinct intestinal subregions suggesting iron trafficking between different cells inside the animal. Spectroscopic signals from the biological samples were compared to purified Drosophila and horse spleen ferritin and to chemically synthesized BPS-iron and BPS-manganese complexes. The results corroborated the presence of BPS-iron in a newly identified ferric iron reductase region of the intestine, which we propose constitutes the major site of iron absorption in this organism.

EPR↗
DOE OSTI2026

PlantCV v4: Image analysis software for high‐throughput plant phenotyping

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data, and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection.

Schuhl, Haley [Donald Danforth Plant Science Cente↗