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DOE OSTI2024

Plasticity of the Arabidopsis leaf lipidome and proteome in response to pathogen infection and heat stress

Abstract Plants must cope with a variety of stressors during their life cycle, and the adaptive responses to these environmental cues involve all cellular organelles. Among them, comparatively little is known about the contribution of cytosolic lipid droplets (LDs) and their core set of neutral lipids and associated surface proteins to the rewiring of cellular processes in response to stress. Here, we analyzed the changes that occur in the lipidome and proteome of Arabidopsis (Arabidopsis thaliana) leaves after pathogen infection with Botrytis cinerea or Pseudomonas syringae, or after heat stress. Analyses were carried out in wild-type plants and the oil-rich double mutant trigalactosyldiacylglycerol1-1 sugar dependent 1-4 (tgd1-1 sdp1-4) that allowed for an allied study of the LD proteome in stressed leaves. Using liquid chromatography-tandem mass spectrometry-based methods, we showed that a hyperaccumulation of the primary LD core lipid TAG is a general response to stress and that acyl chain and sterol composition are remodeled during cellular adaptation. Likewise, comparative analysis of the LD protein composition in stress-treated leaves highlighted the plasticity of the LD proteome as part of the general stress response. We further identified at least two additional LD-associated proteins, whose localization to LDs in leaves was confirmed by confocal microscopy of fluorescent protein fusions. Taken together, these results highlight LDs as dynamic contributors to the cellular adaptation processes that underlie how plants respond to environmental stress.

Plant Sciences↗

DOE OSTI2025

Long Island Steatite Sourcing from Rhode Island Quarries During the Late Holocene Era

This study aimed to investigate the possible sourcing of Long Island steatite artifacts from quarries in Rhode Island. Seven steatite samples from archeological sites on Long Island including Nassau County, Suffolk County (North Fork and South Fork) and Shelter Island were compared to two Rhode Island quarry sample putative sources using X-ray fluorescence (XRF) microscopy at the Submicron Resolution X-ray spectroscopy (SRX) beamline of the National Synchrotron Light Source II at Brookhaven National Laboratory. The site-derived steatite samples displayed numerous similarities in elemental composition compared to the two Rhode Island quarries, Oaklawn and Ochee Springs. This study provides new evidence to support the possible sourcing of Long Island steatite from Rhode Island during the late Holocene era.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Long Island Steatite Sourcing from Rhode Island Quarries During the Late Holocene Era

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography

The dysfunction of α and β cells in pancreatic islets can lead to diabetes. Many questions remain on the subcellular organization of islet cells during the progression of disease. Existing three-dimensional cellular mapping approaches face challenges such as time-intensive sample sectioning and subjective cellular identification. To address these challenges, we have developed a subcellular feature-based classification approach, which allows us to identify α and β cells and quantify their subcellular structural characteristics using soft X-ray tomography (SXT). We observed significant differences in whole-cell morphological and organelle statistics between the two cell types. Additionally, we characterize subtle biophysical differences between individual insulin and glucagon vesicles by analyzing vesicle size and molecular density distributions, which were not previously possible using other methods. These sub-vesicular parameters enable us to predict cell types systematically using supervised machine learning. We also visualize distinct vesicle and cell subtypes using Uniform Manifold Approximation and Projection (UMAP) embeddings, which provides us with an innovative approach to explore structural heterogeneity in islet cells. This methodology presents an innovative approach for tracking biologically meaningful heterogeneity in cells that can be applied to any cellular system.

3D cell mapping↗

DOE OSTI2025

Self‐Assembly Methods Induce Different Individual‐Polymer‐Block Solvation Responses

An understanding of block-specific responses to stimuli in self-assembled copolymers is essential for the effective design of responsive materials. Here, materials formed from different post-reaction processing methods of the same ROMP block copolymer exhibit different block-specific solvent responses, as characterized in situ by fluorescence lifetime imaging microscopy (FLIM). FLIM data were acquired by tagging the polar or nonpolar block separately with a covalently incorporated viscosity-sensitive fluorescent molecular rotor to measure the changing tightness or looseness of assembly upon changes in solvent composition. Rapid precipitation from an insoluble solvent to form a film results in tighter assembly and less difference in tightness/looseness between the two blocks. Further, it interrupts individual block-solvent response behavior. Both results indicate an apparent disruption of the core–shell assembly. This model from FLIM is further supported by differential scanning calorimetry (DSC) and small-angle X-ray scattering (SAXS) data from isolated solids, which show tighter long-range interactions and more long-range order in these kinetically trapped states. Here, the experiments develop FLIM as a method for pinpointing stimuli-responsive behaviors from different processing methods to individual blocks. Together these outcomes provide a future handle for tailoring solvent-triggered assembly/disassembly behavior.

López, Pía A. [University of California, Irvine, C↗

DOE OSTI2026

Quantum Light Imaging of the Plant Root─Rhizobacteria─System Using iLOV Fluorescence

It has been demonstrated recently that the use of specific quantum states of light for two-photon microscopy can lead to a substantial reduction of the intensity of light needed for the imaging of biological objects. This opens new ways to better understand the delicate mechanisms of the interactions of living organisms in the rhizosphere on an extended time scale without optical damage or alteration of their native behavior. Herein, we report a successful realization of entangled two-photon excited fluorescence microscopy of wheat plant roots and a set of biological samples, including purified iLOV protein, bacterial cells expressing iLOV, and combination of these under an extremely low excitation intensity. The entangled two-photon coupling strength of iLOV was modeled using electronic structure calculations which demonstrated that the FMN chromophore in the iLOV protein has an entangled two-photon absorption (ETPA) cross section that is large enough for imaging using weak quantum light for fluorescence excitation. Successful imaging of plant-associated Pantoea sp. YR343 cells expressing iLOV validates the feasibility of using iLOV as a molecular label for characterizing plant-microbe interactions based on entangled photon imaging. In conclusion, the results demonstrate the advantageous use of entangled photon imaging under noninvasive and nondestructive conditions.

Varnavksi, Oleg [Univ. of Michigan, Ann Arbor, MI ↗

DOE OSTI2024

A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging

Abstract Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7× increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca 2+ responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca 2+ concentration using fluorescence lifetime imaging microscopy (FLIM).

Biochemistry & Molecular Biology↗

DOE OSTI2025

Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13 C enrichment in microorganisms, highlighting the potential to directly couple D 2 O or 13 C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.

36 MATERIALS SCIENCE↗

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

Formation of zinc carbonate phases on dissolving calcite, aragonite, and vaterite in acidic aqueous solutions

Calcium carbonate (CaCO 3 ) minerals serve as a major sink to retain metal ions through mineral-water interfacial reactions in which the capacity and long-term stability of contaminant uptake are influenced by coupled dissolution and precipitation reactions of both primary and secondary carbonate minerals (i.e., mineral replacement). Notably, recent studies of calcite reactivity in acidic solutions containing high levels of metal ions demonstrated complex behavior under conditions of sustained disequilibrium. Here, we explored the reactivity of three CaCO 3 polymorphs (calcite, aragonite, and vaterite) with acidic Zn 2+ -containing aqueous solutions using a suite of imaging techniques including optical and scanning electron microscopies, synchrotron-based micro X-ray fluorescence, and transmission X-ray microscopy. Zn uptake by calcite occurred through a two-step process: the formation of a thin layer of the zinc precipitate on the substrate surface followed by the growth of fibrous and radiating hydrozincite particles from the layer. In contrast, Zn uptake by aragonite occurred by mineral replacement where the secondary Zn carbonate phase preserved the external morphology of the original crystal (i.e., a pseudomorph). The replacement of vaterite by hydrozincite occurred within the confined space beneath the porous shell of vaterite, signifying that the primary mechanism driving Zn carbonate precipitation was chemical exchange through the pores. When multiple CaCO 3 polymorphs coexisted, the replacement of aragonite and vaterite occurred preferentially over that of calcite. These results demonstrate the distinct morphological and mineralogical controls over the reactivities of calcium carbonate minerals with Zn 2+ under acidic conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Multiphoton and Harmonic Imaging of Microarchitected Materials

Microadditive manufacturing has revolutionized the production of complex, nano- to microscale components across various fields. This work investigates two-photon (2P) and three-photon (3P) fluorescence imaging, as well as third-harmonic generation (THG) microscopy, to examine periodic microarchitected lattice structures fabricated using multiphoton lithography (MPL). By immersing the structures in refractive index matching fluids, we demonstrate high-fidelity 3D reconstructions of both fluorescent structures using 2P and 3P microscopy as well as low-fluorescence structures using THG microscopy. These results show that multiphoton fluorescence (MPF) imaging offers reduced signal decay with respect to depth compared to single-photon techniques in the examined structures. We further demonstrate the ability to nondestructively identify intentional internal modifications of the structure that are not immediately visible with scanning electron microscope (SEM) images and compression-induced fractures, highlighting the potential of these techniques for quality control and defect detection in microadditively manufactured components.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Influence of Water, Vacuum, and Temperature on Surface Conditions of a Zeolite‐based Molecular Sieve

Molecular sieves such as zeolite-based materials are ubiquitous in industrial separation processes. However, there is a significant gap in understanding the surface properties and adsorption mechanisms for commercial zeolites, as most research focuses on pure zeolite powders rather than industrially relevant forms. Here, this work addresses this gap in understanding by employing advanced characterization techniques, including positron annihilation spectroscopy, X-ray diffraction, scanning electron microscopy, X-ray fluorescence spectroscopy, X-ray photoelectron spectroscopy, liquid nitrogen sorption, and Fourier-transform infrared spectroscopy, to investigate the adsorption and desorption behavior of water in commercial zeolite 13X. Our research reveals insights into the pore-filling mechanisms, the impact of material binders on adsorption properties, and the dynamics of hydration and drying processes for zeolites. Monitoring changes on a minute scale allowed the distinction between fast and slow processes leading to sample drying. The identification of positronium bound to Na + ions indicated that water molecules remain in the vicinity of Na + ions after air-drying zeolite 13X. These findings highlight the importance of various environmental conditions in restoring zeolite properties to baseline after hydration, with significant implications for optimizing industrial processes. This work sets the direction for further research aimed at developing more efficient and robust separation techniques.

Beads Binder↗

DOE OSTI2026

Suppressing Phase Segregation and Improving Stability in Mixed-Halide Perovskites through Spinel Oxide-Directed Epitaxy

Mixed-cation mixed-halide perovskite compositions are essential for achieving the required bandgaps for high-efficiency multijunction photovoltaics, yet their stability remains limited by interfacial defects, phase segregation, and degradation. Here, we introduce spinel oxides as a new family of lattice-matched substrates that enable crystalline, phase-pure, compositionally-uniform, bromide-rich perovskite film growth. The effect of spinel oxides is two-fold: reducing defects at the bottom interface by templating film growth and inducing beneficial compressive strain through mismatch-dependent substrate-perovskite lattice coupling. Spinel oxide substrates facilitate growth of highly crystalline films and eliminate detrimental secondary phases across thicknesses. Using grazing incidence X-ray diffraction, X-ray fluorescence, cathodoluminescence–scanning electron microscopy, cryogenic photoluminescence, and density functional theory, we reveal that Mg-halide bonds at the bottom interface induce lattice mismatch-dependent compressive strain that suppresses halide segregation and further reduces defect formation. In addition, films grown on spinel oxides maintain over 87% of the perovskite phase after 12 h under 100% relative humidity, as monitored by in situ grazing incidence wide-angle X-ray scattering (GIWAXS), compared to less than 70% for control samples. This work extends lattice matching from vapor-deposited epitaxial semiconductors to solution-processed halide perovskites to establish a broadly applicable strategy for defect suppression, phase homogenization, and long-term stability. Based on the fundamental science explored here, we set the stage for the development of lattice-matched spinel oxide charge transport layers to be integrated into perovskite solar cells and other optoelectronic devices.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Hg Accumulation by Single-Cell Sulfate-Reducing Bacteria Methylating Mercury

Methylmercury (MeHg) is a potent neurotoxin that poses risks to ecosystems and human health. MeHg is produced by microbes following saturating-like kinetics. We hypothesize that this saturation reflects a limited intracellular mercury (Hg) accumulation. Here, in this study, we investigated Hg accumulation in Pseudodesulfovibrio hydrargyri BerOc1, a sulfate-reducing model strain able to methylate Hg. Cells were incubated with 0.5 and 2 μM of mercury (HgCl 2 ), and mercury localization was studied using synchrotron-based nano-X-ray fluorescence and high-resolution analytical electron microscopy. For both concentrations, Hg was detected in the bacterial cytosol, in addition to extracellular (Hg, S)-containing nanoparticles. Intracellular Hg levels were slightly higher at 2 μM than at 0.5 μM (1.61 vs 1.40 pg.mm –2 ), suggesting a regulated accumulation. However, the population exhibited heterogeneity in Hg accumulation, particularly at the highest Hg exposure, with some cells being Hg hyperaccumulators. Correlative imaging between Hg localization and cell viability revealed that these hyperaccumulating cells were non-active. Our results suggest that active cells regulate Hg accumulation. From an analytical perspective, a minor subpopulation of hyperaccumulating cells can bias bulk measurements and should be considered in interpreting Hg accumulation in microorganisms. Environmentally, these cells can impact Hg cycling by acting as a metal sink.

Intracellular accumulation↗

DOE OSTI2025

A fluorescent-protein spin qubit

Quantum bits (qubits) are two-level quantum systems that support initialization, readout and coherent control1. Optically addressable spin qubits form the foundation of an emerging generation of nanoscale sensors. The engineering of these qubits has mainly focused on solid-state systems. However, fluorescent proteins, rather than exogenous fluorescent probes, have become the gold standard for in vivo microscopy because of their genetic encodability. Although fluorescent proteins possess a metastable triplet state, they have not been investigated as qubits. Here we realize an optically addressable spin qubit in enhanced yellow fluorescent protein. A near-infrared laser pulse enables triggered readout of the triplet state with up to 20% spin contrast. Using coherent microwave control of the enhanced-yellow-fluorescent-protein spin at liquid-nitrogen temperatures, we measure a (16 ± 2) μs coherence time under Carr–Purcell–Meiboom–Gill decoupling. We express the qubit in mammalian cells, maintaining contrast and coherent control despite the complex intracellular environment. Finally, we demonstrate optically detected magnetic resonance in bacterial cells at room temperature with contrast up to 8%. Our results introduce fluorescent proteins as a powerful qubit platform that paves the way for applications in the life sciences, such as nanoscale field sensing and spin-based imaging modalities.

Feder, Jacob S. [Univ. of Chicago, IL (United Stat↗

DOE OSTI2026

Mechanistic transition of stainless steel 304L corrosion in MgCl 2 phase change material under thermal cycling

Magnesium chloride (MgCl 2 )-based molten salt phase change materials (PCMs) are promising candidates for thermal energy storage (TES) owing to their advantageous thermophysical properties, however, their high corrosivity in the molten state limits material compatibility. In this study, the corrosion behavior of 304?L stainless steel (SS304L) exposed to MgCl2 PCM was investigated as a function of thermal cycling (up to 9000 cycles) relevant to PCM-based TES systems. Microstructural changes and elemental redistribution at the alloy-salt interface under thermal cycling conditions were characterized using synchrotron-based X-ray fluorescence (XRF) and scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM-EDS). Results show that corrosion is governed by selective Cr-dissolution and elemental diffusion near the interface and grain boundaries. A clear transition in the dominant corrosion mechanism is observed with increasing thermal cycles. Surface corrosion is the dominant mechanism up to 1000 cycles, whereas intergranular corrosion becomes the primary degradation mode beyond 2000 cycles. These mechanistic changes are interpreted in terms of evolving interfacial chemistry, microstructure and the diffusion-driven redistribution of alloying elements.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Dynamic Surface Incorporation of Pb 2+ Ions at the Actively Dissolving Calcite (104) Surface

The reaction of dissolved Pb 2+ with calcite surfaces at near-equilibrium conditions involves adsorption of Pb 2+ and precipitation of secondary heteroepitaxial Pb-carbonate minerals. A more complex behavior is observed under far-from-equilibrium conditions, including strong inhibition of calcite dissolution, development of microtopography, and near-surface incorporation of multiple monolayers (ML) of Pb 2+ without precipitation of secondary phases [where 1 ML ≡ 1 Ca/20.2 Å 2 , the crystallographic site density of the calcite (104) lattice plane]. However, the mechanistic controls governing far-from-equilibrium reactivity are not well understood. Here, in this study, we observe the interfacial incorporation of dissolved Pb 2+ during the dissolution of calcite (104) surfaces at pH ~3.7 in a flow-through reaction cell, revealing the formation of a ~1 nm thick Pb-rich calcite layer with a total Pb coverage of ~1.4 ML. These observations of the sorbed Pb distribution used resonant anomalous X-ray reflectivity, X-ray fluorescence, and nanoinfrared atomic force microscopy. We propose that this altered surface layer represents a novel sorption mode that is stabilized by conditions of sustained disequilibrium. This behavior may significantly impact the transport of dissolved metals during disequilibrium processes occurring in acid mine drainage and subsurface CO 2 injection and, if appropriately accounted for, could improve the predictive capability of geochemical reactive-transport models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Three-dimensional characterization of modifications in sapphire exposed to laser-induced damage using multimodal spectral microimaging

Sapphire (Al 2 O 3 ) is a commonly used dielectric material with many applications in lasers and optical systems. Owing to its high resistivity to laser induced damage, it is particularly suitable for use in high power laser systems. This work focuses on developing techniques to characterize material modifications in sapphire. These techniques were applied following localized laser induced ablation, commonly referred to as laser-damage, resulting from exposure to single 100-ps and 6-ns pulses. Measurements of fluorescence-based piezospectroscopy and confocal Raman microscopy were performed with spatial resolution on the order of 1 μ m. Raman microscopy reveals that the relaxation of material exposed to the rapid laser heating, elastic and viscoplastic deformation, melting, and solidification leads to the formation of a polycrystalline material phase. In addition, narrowband fluorescence lines, referred to as R 1 and R 2 , exhibit pressure-sensitive changes to their spectral profiles, allowing 3D internal stresses to be recorded with spatial resolution of the order of a few micrometers.

Laser-damage↗