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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Cryo-EM visualization of viruses from partially irrigated soils

Viruses are numerically the most abundant forms on Earth, and most are present in soil. Even though viruses are highly abundant in soil and critical to rhizosphere function, visualizing the diverse morphotypes within soil has been challenging. The difficulty is primarily due to the heterogenous nature of isolated suspensions that typically contain nanometer to micron scale debris which renders protein crystallography for structural studies unfeasible and hinders cryo-electron microscopy due to ice thickness and contrast issues. Here we employed and compared a simple spin filtration method to cleanup solutions of extracted viruses for direct observation with cryo-electron microscopy. The method employs common physical biochemical separation steps to remove large and small debris which dramatically improves image quality and preservation of structural features to permit visualizing morphotypes not typically seen with conventional negative stain approaches. In addition to tailed and non-tailed polyhedral phages, several under reported or novel morphotypes of soil viruses are directly visualized as a particle library with both 2D and 3D information.

cryo-EM↗
DOE OSTI2026

Cryo-EM Grid Screening Tool

Explore the source record for details and available documents.

cryo-EM, grid screening, vitrification, electron m↗
DOE OSTI2026

Automated Bacterial Identification and Morphological Feature Analysis in Low‐Dose Cryo‐EM Using YOLOv11

Bacteria rapidly adapt to environmental cues through morphological and ultrastructural changes that correlate with physiology and behavior. Cryogenic transmission electron microscopy (cryo‐TEM) can capture these phenotypic changes in near‐native, vitrified states, but manual analysis of low‐dose micrographs is labor intensive and limits throughput. Here, we present an end‐to‐end workflow that combines low‐dose cryo‐TEM imaging with a YOLOv11‐based instance‐segmentation model to automatically identify bacteria and quantify key structural features directly from the micrographs. This workflow enables (i) robust bacterial localization and counting from low‐magnification atlas/montage images, (ii) automated measurements of cell‐envelope (outer–inner membrane) thickness and anisotropy from higher‐magnification views, and (iii) detection and quantification of bacteria–flagella interactions, including overlap length and curvature metrics for interacting versus noninteracting flagella. Using Pantoea sp. YR343 grown under distinct media conditions, we show that the automated measurements agree with manual annotations while substantially reducing analysis time. Together, these tools provide a practical framework for scalable bacterial identification and quantitative phenotyping in low‐dose cryo‐TEM datasets and establish a foundation for extending cryo‐TEM image analysis toward higher‐throughput studies of microbial heterogeneity and biointerfaces.

YOLOv11↗
DOE OSTI2025

Cryo-EM structures of the small-conductance Ca 2+ -activated K Ca 2.2 channel

Small-conductance Ca 2+ -activated K + (K Ca 2.1-K Ca 2.3) channels modulate neuronal and cardiac excitability. We report cryo-electron microscopy structures of the K Ca 2.2 channel in complex with calmodulin and Ca 2+ , alone or bound to two small molecule inhibitors, at 3.18, 3.50, 2.99 and 2.97 angstrom resolution, respectively. Extracellular S3-S4 loops in β-hairpin configuration form an outer canopy over the pore with an aromatic box at the canopy’s center. Each S3-S4 β-hairpin is tethered to the selectivity filter in the neighboring subunit by inter-subunit hydrogen bonds. This hydrogen bond network flips the aromatic residue (Tyr362) in the filter’s GYG signature by 180°, causing the outer selectivity filter to widen and water to enter the filter. Disruption of the tether by a mutation narrows the outer selectivity filter, realigns Tyr362 to the position seen in other K + channels, and significantly increases unitary conductance. UCL1684, a mimetic of the bee venom peptide apamin, sits atop the canopy and occludes the opening in the aromatic box. AP14145, an analogue of a therapeutic for atrial fibrillation, binds in the central cavity below the selectivity filter and induces closure of the inner gate. These structures provide a basis for understanding the small unitary conductance and pharmacology of K Ca 2.x channels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR

Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an architecture remain a mystery. Using cryoelectron microscopy we capture snapshots of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase (DPOR) during substrate binding and turnover. DPOR catalyzes reduction of the C17 = C18 double bond in protochlorophyllide during the dark chlorophyll biosynthetic pathway. DPOR is composed of electron donor (L-protein) and acceptor (NB-protein) component proteins that transiently form a complex in the presence of ATP to facilitate ET. NB-protein is an α 2 β 2 heterotetramer with two structurally identical halves. However, our structures reveal that NB-protein becomes functionally asymmetric upon substrate binding. Asymmetry results in allosteric inhibition of L-protein engagement and ET in one half. Residues that form a conduit for ET are aligned in one half while misaligned in the other. An ATP hydrolysis-coupled conformational switch is triggered once ET is accomplished in one half. These structural changes are then relayed to the other half through a di-nuclear copper center at the tetrameric interface of the NB-protein and leads to activation of ET and substrate reduction. These findings provide a mechanistic blueprint for regulation of long-range electron transfer reactions.

Computational biophysics↗
DOE OSTI2024

Cryo-EM confirms a common fibril fold in the heart of four patients with ATTRwt amyloidosis

ATTR amyloidosis results from the conversion of transthyretin into amyloid fibrils that deposit in tissues causing organ failure and death. This conversion is facilitated by mutations in ATTRv amyloidosis, or aging in ATTRwt amyloidosis. ATTRv amyloidosis exhibits extreme phenotypic variability, whereas ATTRwt amyloidosis presentation is consistent and predictable. Previously, we found unique structural variabilities in cardiac amyloid fibrils from polyneuropathic ATTRv-I84S patients. In contrast, cardiac fibrils from five genotypically different patients with cardiomyopathy or mixed phenotypes are structurally homogeneous. To understand fibril structure’s impact on phenotype, it is necessary to study the fibrils from multiple patients sharing genotype and phenotype. Here we show the cryo-electron microscopy structures of fibrils extracted from four cardiomyopathic ATTRwt amyloidosis patients. Our study confirms that they share identical conformations with minimal structural variability, consistent with their homogenous clinical presentation. Our study contributes to the understanding of ATTR amyloidosis biopathology and calls for further studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Two datasets are better than one: method of double moments for 3D reconstruction in cryo-EM

Cryo-electron microscopy is a powerful imaging technique for reconstructing three-dimensional molecular structures from noisy tomographic projection images of randomly oriented particles. We introduce a new data fusion framework, termed the method of double moments, which reconstructs molecular structures from two instances of the second-order moment of projection images obtained under distinct orientation distributions: one uniform, the other non-uniform and unknown. We prove that these moments generically uniquely determine the underlying structure, up to a global rotation and reflection, and we develop a convex-relaxation-based algorithm that achieves accurate recovery using only second-order statistics. Our results demonstrate the advantage of collecting and modeling multiple datasets under different experimental conditions, illustrating that leveraging dataset diversity can substantially enhance reconstruction quality in computational imaging tasks.

Kam’s method↗
DOE OSTI2025

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting

Abstract The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.

Jaiswal, Rahul↗
DOE OSTI2025

Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex

Abstract Nitrogenases are metalloenzymes that catalyze the reduction of atmospheric dinitrogen to ammonia, sustaining the global nitrogen cycle. While bacterial nitrogenase has been extensively characterized, the architecture and regulation of archaeal nitrogenases remain unknown despite longstanding evidence of nitrogen fixation in methanogens. Here we report a 3.1 Å cryo-electron microscopy structure of a native nitrogenase–PII protein supercomplex from Methanosarcina acetivorans. The structure reveals an unprecedented assembly of three NifDK heterotetramers bridged by six NifI1,2 heterotrimeric PII complexes, which sterically block NifH association and lock the enzyme in an inactive state. The NifI complexes display asymmetric binding of ADP and 2-oxoglutarate, coupling nitrogenase inhibition directly to cellular energy and nitrogen status. Addition of 2-oxoglutarate and ATP releases the NifI complexes, stimulating a threefold increase in NifDK activity in vitro. This higher-order architecture uncovers a previously unrecognized regulatory strategy in methanogens, in which PII proteins drive nitrogenase oligomerization to control activity. The discovery that nitrogenase activity may be modulated through direct assembly into higher-order structures opens new avenues for exploring nitrogenase evolution, regulation, and biotechnological applications. One sentence summary Discovery of a nitrogenase-PII protein supercomplex in methanogens, uncovering a metabolite-gated assembly mechanism for nitrogenase inhibition.

Nitrogenase, Electron Transfer, Methanogen↗
DOE OSTI2025

EM-Enhanced HyPOR Loop for Fast Fusion Cycles

Vacuum pumps are the heart of a fusion energy facility – fusion power cannot be generated without them. Nevertheless, the vacuum technology needed to operate a viable fuel cycle for a compact fusion power plant does not exist. Commercial vacuum technology offers the best solution to this challenge, but a pump oil recycling and detritiation system is necessary. Conventional oil detritiation processes have only been developed to deal with legacy waste and are too slow and destructive to the oil. Further, post hoc detritiation strategies are intrinsically inefficient. Our approach is to rethink the challenge holistically by designing the pumping fluid and tritium extraction system in an integrated manner to achieve an innovative solution. By selecting an oil for the specific task of pumping tritium and then designing our catalytic system to selectively target the tritium-bearing functional groups, an effective detritiation system (hydrocarbon pump oil recycling, HyPOR, loop) for fusion power plants can be obtained. The project demonstrated a HyPOR loop process that can selectively remove heavier hydrogen isotopes from pump oil, reaching the target of 99.5 % removal, with an uptake of less than 0.01% of tritium throughput, while also purifying the oil of radiation-induced damage. The recycled oil retained its pumping characteristics over 7 recycles and gamma irradiation over 30 MGy. By meeting these targets, the project enable a reduction in pump operational costs from $\$$14.5M/year to $\$$103k/year (>140× reduction), reducing pump electric power consumption from 2.8 MW to 0.25 MW (>10× reduction), and reducing in-process tritium inventory from 2.03 kg to 0.48 kg (>4× reduction).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗