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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Helium Ion Microscopy

Nanotechnology research led to the development of various instruments to be used for imaging or fabrication. The helium ion microscope (HIM) became available in 2006 but quickly gained popularity. Its unique gas field ion source enables high-resolution imaging, nanofabrication, direct write, and the recent combination with a secondary ion mass spectrometer offers chemical imaging with ~15 nm resolution. Particularly attractive are the small interaction volume of He and Ne (the two gases offered), small beam spot size, and a moderate sputtering rate. Additionally, the HIM is an excellent imaging tool for insulating samples in soft, polymeric, and biological materials. It can be expected that helium ion microscopy will continue to have a strong influence on broad range of scientific disciplines, including chemistry, materials science, and biology.This chapter aims at providing an overview of the current status of HIM for imaging, analysis, and nanofabrication. It introduces the reader to key components of the instrument, theoretical background, and latest results in the areas of imaging, material fabrication, and chemical analysis capabilities of helium ion microscopy.

Belianinov, Alex↗
DOE OSTI2021

Preserved and variable spatial‐chemical changes of lipids across tomato leaves in response to central vein wounding reveals potential origin of linolenic acid in signal transduction cascade

Abstract Membrane lipids serve as substrates for the generation of numerous signaling lipids when plants are exposed to environmental stresses, and jasmonic acid, an oxidized product of 18‐carbon unsaturated fatty acids (e.g., linolenic acid), has been recognized as the essential signal in wound‐induced gene expression. Yet, the contribution of individual membrane lipids in linolenic acid generation is ill‐defined. In this work, we performed spatial lipidomic experiments to track lipid changes that occur locally at the sight of leaf injury to better understand the potential origin of linolenic and linoleic acids from individual membrane lipids. The central veins of tomato leaflets were crushed using surgical forceps, leaves were cryosectioned and analyzed by two orthogonal matrix‐assisted laser desorption/ionization mass spectrometry imaging platforms for insight into lipid spatial distribution. Significant changes in lipid composition are only observed 30 min after wounding, while after 60 min lipidome homeostasis has been re‐established. Phosphatidylcholines exhibit a variable pattern of spatial behavior in individual plants. Among lysolipids, lysophosphatidylcholines strongly co‐localize with the injured zone of wounded leaflets, while, for example, lysophosphatidylglycerol (LPG) (16:1) accumulated preferentially toward the apex in the injured zone of wounded leaflets. In contrast, two other LPGs (LPG [18:3] and LPG [18:2]) are depleted in the injured zone. Our high‐resolution co‐localization imaging analyses suggest that linolenic acids are predominantly released from PCs with 16_18 fatty acid composition along the entire leaf, while it seems that in the apex zone PG (16:1_18:3) significantly contributes to the linolenic acid pool. These results also indicate distinct localization and/or substrate preferences of phospholipase isoforms in leaf tissue.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue

Myelin insulates neuronal axons and enables fast signal transmission, constituting a key component of brain development, aging and disease. Yet, myelin-specific imaging of macroscopic samples remains a challenge. Here, we exploit myelin’s nanostructural periodicity, and use small-angle X-ray scattering tensor tomography (SAXS-TT) to simultaneously quantify myelin levels, nanostructural integrity and axon orientations in nervous tissue. Proof-of-principle is demonstrated in whole mouse brain, mouse spinal cord and human white and gray matter samples. Outcomes are validated by 2D/3D histology and compared to MRI measurements sensitive to myelin and axon orientations. Specificity to nanostructure is exemplified by concomitantly imaging different myelin types with distinct periodicities. Finally, we illustrate the method’s sensitivity towards myelin-related diseases by quantifying myelin alterations in dysmyelinated mouse brain. This non-destructive, stain-free molecular imaging approach enables quantitative studies of myelination within and across samples during development, aging, disease and treatment, and is applicable to other ordered biomolecules or nanostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A Molecular-MNIST Dataset for Machine Learning Study on Diffraction Imaging and Microscopy

An image dataset of 10 different size molecules, where each molecule has 2,000 structural variants, is generated from the 2D cross-sectional projection of Molecular Dynamics trajectories. The purpose of this dataset is to provide a benchmark dataset for the increasing need of machine learning, deep learning and image processing on the study of scattering, imaging and microscopy.

BASIC BIOLOGICAL SCIENCES,OTHER INSTRUMENTATION↗
DOE OSTI2026

Desorption Electrospray Ionization–Mass Spectrometry Imaging Provides Spatiochemical Information on Potential Biocontrol Agents against Phytophthora capsici Infection in Tomato Plants

Biological control agents can offer an eco-friendly and more sustainable alternative to conventional chemical pesticides, providing protection against destructive pathogens, such as Phytophthora capsici, while reducing potential environmental harm associated with synthetic pesticide use in agricultural systems. This work evaluates the biocontrol effectiveness of Bacillus vallismortis, Bacillus amyloliquefaciens, Bacillus thuringiensis, and Bacillus subtilis, against the widespread plant pathogen Phytophthora capsici. Our studies showed that Bacillus thuringiensis and Bacillus subtilis promote plant growth and provide protection against Phytophthora capsici in both in vitro and in vivo greenhouse studies, while Bacillus vallismortis and Bacillus amyloliquefaciens were effective in vitro but not in vivo. Specifically, Bacillus thuringiensis was observed to both hinder the growth of Phytophthora capsici and enhance plant resilience to this pathogen, with B. thuringiensis-treated, pathogen-exposed plants displaying a 94.4% increase in root length and a 74.0% increase in shoot height compared to plants with only oomycete exposure. To probe the molecular interactions between the biocontrol agent and pathogen, a dual culture of Bacillus thuringiensis and Phytophthora capsici was analyzed in situ using a desorption electrospray ionization–mass spectrometry imaging (DESI-MSI) workflow. This approach interrogated the spatially oriented biochemical interactions that may serve as the molecular foundation for the effectiveness of these biological control agents in crop protection, identifying seven unique phenotypic regions within the dual culture. Herein, we demonstrate the benefits of biological control agent application in tomato cultivation and showcase the strengths of desorption electrospray ionization–mass spectrometry imaging when applied to the spatially resolved molecular characterization of agriculturally relevant microorganisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A bi-channel aided stitching of atomic force microscopy images

Microscopy is an essential tool in scientific research, enabling the visualization of structures at micro- and nanoscale resolutions. However, the field of microscopy often encounters limitations in field-of-view (FOV), restricting the amount of sample that can be imaged in a single capture. To overcome this limitation, image stitching techniques have been developed to seamlessly merge multiple overlapping images into a single, high-resolution composite. The images collected from microscope need to be optimally stitched before accurate physical information can be extracted from post analysis. However, the existing stitching tools either struggle to stitch images together when the microscopy images are feature sparse or cannot address all the transformations of images when performing image stitching. To address these issues, we propose a bi-channel aided feature-based image stitching method and demonstrate its use on Atomic Force Microscopy (AFM) generated Pantoea sp. YR343 biofilm and PTO thin film sample images as experimental data. The topographical channel image of AFM data captures the morphological details of the sample, and a stitched topographical image is desired for researchers. We utilize the amplitude and phase channels of AFM data to maximize the matching features and to estimate the position of the original topographical images and show that the proposed bi-channel aided stitching method outperforms the traditional direct stitching approach in AFM topographical image stitching task. Here, we demonstrated the application on AFM, but similar approaches could be employed of optical microscopy with brightfield and fluorescence channels. We believe this proposed workflow can serve as a valuable augmentation strategy for microscopy image stitching tasks and will benefit the experimentalist to avoid erroneous analysis and discovery due to incorrect stitching.

Atomic force microscopy↗
DOE OSTI2024

X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation

Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage–cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Synthesis and Evaluation of a Bifunctional Chelator for Thorium-227 Targeted Radiotherapy

Thorium-227 (227Th) is an α-emitting radionuclide currently under investigation for targeted alpha therapy. Available chelators used for this isotope suffer from challenging multistep syntheses. Here, we present the synthesis and preclinical evaluation of a novel bifunctional chelator, p-SCN-Bn-DOTHOPO, which contains an isothiocyanate group that is suitable for conjugation to biological molecules. This bifunctional chelator was prepared with a 26% overall yield in four steps and conjugated to the human epidermal growth factor receptor 2 targeting antibody, trastuzumab. The resulting immunoconjugate was labeled with [227Th]ThIV (pH 5.5, room temperature, 60 min) with ≥95% radiochemical yield and purity. The conjugate was also labeled with zirconium-89 (89Zr), which can be used for positron emission tomography imaging. The radiometal complexes were subsequently investigated for their biological stability. The results described here provide insight into ligand design strategies and optimization of chelators for the development of the next generation of 89Zr and 227Th radiopharmaceuticals.

Thorium↗
DOE OSTI2023

Recurrent and convolutional neural networks for sequential multispectral optoacoustic tomography ( MSOT ) imaging

Abstract Multispectral optoacoustic tomography (MSOT) is a beneficial technique for diagnosing and analyzing biological samples since it provides meticulous details in anatomy and physiology. However, acquiring high through‐plane resolution volumetric MSOT is time‐consuming. Here, we propose a deep learning model based on hybrid recurrent and convolutional neural networks to generate sequential cross‐sectional images for an MSOT system. This system provides three modalities (MSOT, ultrasound, and optoacoustic imaging of a specific exogenous contrast agent) in a single scan. This study used ICG‐conjugated nanoworms particles (NWs‐ICG) as the contrast agent. Instead of acquiring seven images with a step size of 0.1 mm, we can receive two images with a step size of 0.6 mm as input for the proposed deep learning model. The deep learning model can generate five other images with a step size of 0.1 mm between these two input images meaning we can reduce acquisition time by approximately 71%.

Juhong, Aniwat↗
DOE OSTI2021

Mixed Effect Modeling of Dose and Linear Energy Transfer Correlations With Brain Image Changes After Intensity Modulated Proton Therapy for Skull Base Head and Neck Cancer

Intensity modulated proton therapy (IMPT) could yield high linear energy transfer (LET) in critical structures and increased biological effect. For head and neck cancers at the skull base this could potentially result in radiation-associated brain image change (RAIC). The purpose of the current study was to investigate voxel-wise dose and LET correlations with RAIC after IMPT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2025

Spatial Glycomics and Kidney Disease

Glycans are critical for the kidney's physiological and pathological cellular functions, and our ability to reveal their spatial distributions within tissues has helped us reveal how these carbohydrate moieties are involved in many of these processes. This review discusses the role of different types of glycans in kidney biology and disease, common approaches used for glycan imaging, and how glycan imaging has helped us better understand kidney pathology. Here, we mainly focus on emerging methods using mass spectrometry imaging (MSI) because this technology is untargeted and provides complete information on glycan composition compared to the other methods, such as lectin and metabolite labeling, which are targeted and often inform only on the specific part of a glycan structure. We especially focus on protein N-glycosylation, as this is one of the most common post-translational modifications, and these moieties play a vital role in renal structure and function. The recent advancements in MSI of N-glycans we reviewed have provided new insights into the pathophysiology of the kidney and paved the way for clinical application.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Pore architecture and particulate organic matter in soils under monoculture switchgrass and restored prairie in contrasting topography

Bioenergy cropping systems can substantially contribute to climate change mitigation. However, limited information is available on how they affect soil characteristics, including pores and particulate organic matter (POM), both essential components of the soil C cycle. The objective of this study was to determine effects of bioenergy systems and field topography on soil pore characteristics, POM, and POM decomposition under new plant growth. We collected intact soil cores from two systems: monoculture switchgrass (Panicum virgatum L.) and native prairie, at two contrasting topographical positions (depressions and slopes), planting half of the cores with switchgrass. Pore and POM characteristics were obtained using X-ray computed micro-tomography (μCT) (18.2 µm resolution) before and after new switchgrass growth. Diverse prairie vegetation led to higher soil C than switchgrass, with concomitantly higher volumes of 30–90 μm radius pores and greater solid-pore interface. Yet, that effect was present only in the coarse-textured soils on slopes and coincided with higher root biomass of prairie vegetation. Surprisingly, new switchgrass growth did not intensify decomposition of POM, but even somewhat decreased it in monoculture switchgrass as compared to non-planted controls. Our results suggest that topography can play a substantial role in regulating factors driving C sequestration in bioenergy systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Many but not all deep neural network audio models capture brain responses and exhibit correspondence between model stages and brain regions

Models that predict brain responses to stimuli provide one measure of understanding of a sensory system and have many potential applications in science and engineering. Deep artificial neural networks have emerged as the leading such predictive models of the visual system but are less explored in audition. Prior work provided examples of audio-trained neural networks that produced good predictions of auditory cortical fMRI responses and exhibited correspondence between model stages and brain regions, but left it unclear whether these results generalize to other neural network models and, thus, how to further improve models in this domain. We evaluated model-brain correspondence for publicly available audio neural network models along with in-house models trained on 4 different tasks. Most tested models outpredicted standard spectromporal filter-bank models of auditory cortex and exhibited systematic model-brain correspondence: Middle stages best predicted primary auditory cortex, while deep stages best predicted non-primary cortex. However, some state-of-the-art models produced substantially worse brain predictions. Models trained to recognize speech in background noise produced better brain predictions than models trained to recognize speech in quiet, potentially because hearing in noise imposes constraints on biological auditory representations. The training task influenced the prediction quality for specific cortical tuning properties, with best overall predictions resulting from models trained on multiple tasks. The results generally support the promise of deep neural networks as models of audition, though they also indicate that current models do not explain auditory cortical responses in their entirety.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural Connectivity-Based Parcellation of the Dopaminergic Midbrain in Healthy Subjects and Schizophrenic Patients

Background and objectives: Functional deregulation of dopaminergic midbrain regions is a core feature of schizophrenia pathophysiology. Anatomical research on primates suggests that these regions may be subdivided into distinct, topographically organized functional territories according to their connectivity to the striatum. The aim of the present work was the reconstruction of dopaminergic midbrain subregions in healthy subjects and schizophrenic patients and the evaluation of their structural connectivity profiles. Materials and Methods: A hypothesis-driven connectivity-based parcellation derived from diffusion tractography was applied on 24 healthy subjects and 30 schizophrenic patients to identify distinct territories within the human dopaminergic midbrain in vivo and non-invasively. Results: We identified a tripartite subdivision of dopaminergic midbrain, including limbic, prefrontal and sensorimotor territories. No significant differences in structural features or connectivity were found between subjects and patients. Conclusions: The parcellation scheme proposed herein may help to achieve detailed characterization of structural and functional anomalies of the dopaminergic midbrain in schizophrenic patients.

ventral tegmental area↗
DOE OSTI2021

Mass Spectrometry Imaging of Bio‐oligomer Polydispersity in Plant Tissues by Laser Desorption Ionization from Silicon Nanopost Arrays

Abstract Mass spectrometry imaging (MSI) enables simultaneous spatial mapping for diverse molecules in biological tissues. Matrix‐assisted laser desorption ionization (MALDI) mass spectrometry (MS) has been a mainstream MSI method for a wide range of biomolecules. However, MALDI‐MSI of biological homopolymers used for energy storage and molecular feedstock is limited by, e.g., preferential ionization for certain molecular classes. Matrix‐free nanophotonic ionization from silicon nanopost arrays (NAPAs) is an emerging laser desorption ionization (LDI) platform with ultra‐trace sensitivity and molecular imaging capabilities. Here, we show complementary analysis and MSI of polyhydroxybutyric acid (PHB), polyglutamic acid (PGA), and polysaccharide oligomers in soybean root nodule sections by NAPA‐LDI and MALDI. For PHB, number and weight average molar mass, polydispersity, and oligomer size distributions across the tissue section and in regions of interest were characterized by NAPA‐LDI‐MSI.

Samarah, Laith Z.↗
DOE OSTI2021

Designed and biologically active protein lattices

Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.

77 NANOSCIENCE AND NANOTECHNOLOGY↗