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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Evaluation of a high-throughput method for processing sponge-stick samples to detect viable, non-spore-forming biothreat agents

After a bioterrorism incident, surface sampling is often used to determine the extent of contamination and exposure, guiding decontamination efforts and decisions for re-occupancy of affected sites. The sponge-stick (SS) is a preferred and commonly used device for sample collection to detect both spore-forming and non-spore-forming biothreat agents from non-porous surfaces. Here, in this study, a recently developed high-throughput method (HTM) for processing SS samples to detect viable Bacillus anthracis spores was adapted for detection of non-spore-forming biothreat agents, Yersinia pestis and Francisella tularensis. The scalable HTM was used to process up to 20 SS samples simultaneously, compared to the current stomacher-based method which processes one SS at a time. Comparisons of the HTM and the stomacher-based method were statistically indistinguishable for most experiments (P > 0.05) with HTM recoveries of 37–60 % for Y. pestis inoculated at 102–103 cells/SS and held 48 h at 4 °C to mimic sample transport/storage. The HTM was integrated with Rapid Viability-Polymerase Chain Reaction (RV-PCR) analysis to detect viable Y. pestis in the presence of particulate contamination (Arizona Test Dust, ATD). This approach detected Y. pestis inoculated at 20 cells/SS and ATD did not impact detection (P > 0.05). F. tularensis showed significantly lower recoveries between no-hold time and 48-h hold time (4 °C, P < 0.05) using the HTM, which further testing showed could be due to toxicity of the neutralizing buffer used for SS pre-wetting. With modifications, this method could enhance throughput capacity while maintaining similar recovery efficiencies to current methods for other non-spore-forming bacterial pathogens.

Biological and medical sciences↗
DOE OSTI2024

Implicating the red body of Nannochloropsis in forming the recalcitrant cell wall polymer algaenan

Stramenopile algae contribute significantly to global primary productivity, and one class, Eustigmatophyceae, is increasingly studied for applications in high-value lipid production. Yet much about their basic biology remains unknown, including the nature of an enigmatic, pigmented globule found in vegetative cells. Here, we present an in-depth examination of this “red body,” focusing on Nannochloropsis oceanica. During the cell cycle, the red body forms adjacent to the plastid, but unexpectedly it is secreted and released with the autosporangial wall following cell division. Shed red bodies contain antioxidant ketocarotenoids, and overexpression of a beta-carotene ketolase results in enlarged red bodies. Infrared spectroscopy indicates long-chain, aliphatic lipids in shed red bodies and cell walls, and UHPLC-HRMS detects a C32 alkyl diol, a potential precursor of algaenan, a recalcitrant cell wall polymer. We propose that the red body transports algaenan precursors from plastid to apoplast to be incorporated into daughter cell walls.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cycling ferulate in monocot cell walls

Cell walls in grasses contain arabinoxylan polysaccharides decorated with ferulate groups but the mechanism by which the ferulate is attached to arabinoxylans has long remained unknown. Here, a new study shows that ferulate is transferred to arabinoxylan from a 3,6-di-O-feruloyl sucrose intermediate formed in a sucrose ferulate cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Diatom volatile organic compound production is driven by diel metabolism and the cell cycle

Introduction: Volatile organic compounds (VOCs) are small, low-vapor-pressure molecules emitted from the surface ocean into the atmosphere. In the atmosphere, VOCs can change OH reactivity and condense onto particles to become cloud condensation nuclei. VOCs are produced by phytoplankton, but the conditions leading to VOC accumulation in the surface ocean are poorly understood.Methods: In this study, VOC accumulation was measured in real time over a 12 h day−12 h night cycle in the model diatom Phaeodactylum tricornutum during exponential growth.Results: Sixty-three m/z signals were produced in higher concentrations than in cell-free controls. All VOCs, except methanol, were continuously produced over 24 h. All VOCs accumulated to higher concentrations during the day compared to the night, and 11 VOCs exhibited distinct accumulation patterns during the morning hours. Twenty-seven VOCs were associated with known metabolic pathways in P. tricornutum, with most VOCs involved in amino acid and fatty acid metabolism.Discussion: Patterns of VOC production were strongly associated with diel shifts in cell physiology and the cell cycle. Diel VOC production patterns give a fundamental understanding of the first steps in VOC accumulation in the surface ocean.

Biological and medical sciences↗
DOE OSTI2025

Evaluating size exclusion chromatography for nucleic acid removal in Klebsiella pneumoniae cell surface polysaccharide purification

Cell surface-associated polysaccharides in Klebsiella are major virulence determinants and crucial targets for developing vaccines. Traditionally, the purification of these cell surface polysaccharides from Klebsiella pneumoniae involves a multi-step process comprising phenol extraction, nuclease digestion, ultracentrifugation, and repeated ethanol extractions. In this study, we evaluated size exclusion chromatography for effectively eliminating nucleic acid contamination while purifying high molecular weight cell surface-associated polysaccharides. Post-initial extraction, the nucleic acid content remains significantly elevated, and kinetic analysis reveals that DNase I and RNase A digestion is neither economically viable nor effective for removing these contaminants. Employing an appropriate size exclusion resin removes over 99 % of nucleic acid contamination, as confirmed by nucleic acid content analysis and agarose gel electrophoresis. Purity and structural analysis using 1H 1D-NMR and 2D-NMR demonstrate that the cell surface-associated polysaccharide purified with this study is highly homogeneous and identified as antigenic O-polysaccharide. This approach streamlines the purification process by removing the need for nuclease digestion and additional ethanol precipitation steps.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Kinetics Modeling and Reactor Design Study of Glucose-to-Terpenes Cell-Free Conversion

Cell-free systems offer many advantages over traditional biological conversion by eliminating biological growth constraints. It also offers easy manipulation and finetuning of the reaction conditions for each individual enzyme. The conversion of cellulosic glucose to Limonene, a terpene, is a promising pathway for producing fuels and chemicals. Recent advances in developing cell-free systems focuses on bench scale optimization of terpene yield and to demonstrate its feasibility towards commercialization [1,2]. There is significant knowledge gap regarding reaction kinetics of these cell-free systems to further study how it will perform at larger scale. We present here, our studies on reaction kinetics and reactor design implications of cell-free glucose to Limonene conversion to facilitate the further development and commercialization of this process. We developed a novel kinetic model based on the metabolic-network structure of the cell-free system with multi-substrate reversible Michaelis-Menten rate law. To estimate kinetic parameters for this system of rate equations, we employed Bayesian optimization to perform global search with the assistance of gaussian processes to balance exploration and exploitation. The model parameters estimated showed good results compared with experimental data. The estimated parameters were used to perform sensitivity analysis. We found that Hexokinase is one of the most critical enzymes that affect the conversion of the glucose. We also observed that abundance of co-factors is also critical to the conversion of glucose to limonene. We investigated packed bed reactors with enzymes immobilized on the surface of particles to convert glucose stream into Limonene for larger scale production. The reactor design such as particle size, enzyme loading, and flow rate are found to be critical for improving yields. [1] Dudley, Q.M., Nash, C.J. and Jewett, M.C., 2019. Synthetic Biology, 4(1), p.ysz003. [2] Korman, T.P., Opgenorth, P.H. and Bowie, J.U., 2017. Nature communications, 8(1), p.15526.

09 BIOMASS FUELS↗
DOE OSTI2025

Emergence of lignin-carbohydrate interactions during plant stem maturation visualized by solid-state NMR

Lignification waterproofs and strengthens secondary plant cell walls but increases the energy cost of sugar release for biofuels. The physical association between lignin and the carbohydrate scaffold that accommodates lignin polymerization, along with the distinct roles of lignin units and carbohydrate partners during lignification, remain unclear. Here, we map lignin-carbohydrate spatial proximity by solid-state NMR in 13 C-labeled Arabidopsis inflorescence stems during secondary cell wall formation. Analyses include wild-type plants and mutants that selectively or globally disrupt lignin biosynthesis. Mature walls in basal regions show enrichment of S-lignin and dense carbohydrate-lignin packing. Acetylated xylan predominantly associates with S-lignin, while methylated pectin unexpectedly interacts with G-lignin during early-stage lignification. The importance of S-lignin in stabilizing the carbohydrate-lignin interface is highlighted by weak lignin-carbohydrate contacts and compromised mechanical properties in the low-S fah1 mutant, whereas the ref3 mutant, despite reduced lignin content, remains unaffected due to a high S/G ratio. Thus, molecular mixing patterns, rather than lignin content, critically determine the structure and properties of lignocellulosic materials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis

Copper (Cu) is essential for respiration, neurotransmitter synthesis, oxidative stress response, and transcription regulation, with imbalances leading to neurological, cognitive, and muscular disorders. Here we show the role of a novel Cu-binding protein (Cu-BP) in mammalian transcriptional regulation, specifically on skeletal muscle differentiation using murine primary myoblasts. Utilizing synchrotron X-ray fluorescence-mass spectrometry, we identified murine cysteine-rich intestinal protein 2 (mCrip2) as a key Cu-BP abundant in both nuclear and cytosolic fractions. mCrip2 binds two to four Cu + ions with high affinity and presents limited redox potential. CRISPR/Cas9-mediated deletion of mCrip2 impaired myogenesis, likely due to Cu accumulation in cells. CUT&RUN and transcriptome analyses revealed its association with gene promoters, including MyoD1 and metallothioneins, suggesting a novel Cu-responsive regulatory role for mCrip2. Our work describes the significance of mCrip2 in skeletal muscle differentiation and metal homeostasis, expanding understanding of the Cu-network in myoblasts. Copper (Cu) is essential for various cellular processes, including respiration and stress response, but imbalances can cause serious health issues. This study reveals a new Cu-binding protein (Cu-BP) involved in muscle development in primary myoblasts. Using unbiased metalloproteomic techniques and high throughput sequencing, we identified mCrip2 as a key Cu-BP found in cell nuclei and cytoplasm. mCrip2 binds up to four Cu + ions and has a limited redox potential. Deleting mCrip2 using CRISPR/Cas9 disrupted muscle formation due to Cu accumulation. Further analyses showed that mCrip2 regulates the expression of genes like MyoD1, essential for muscle differentiation, and metallothioneins in response to copper supplementation. This research highlights the importance of mCrip2 in muscle development and metal homeostasis, providing new insights into the Cu-network in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A Prodrug Strategy to Conditionally Trap Therapeutic Payloads for Improved Tumor Retention

Altered extracellular proteolysis has been exploited to selectively activate therapeutics in diseases such as cancer; however, once activated, extracellular drugs can diffuse away, limiting efficacy. We address this challenge by coupling proteolytic activation with membrane tethering to retain drugs within diseased tissue. To accomplish this, we developed “restricted interaction peptides” (RIPs), a delivery platform that leverages elevated proteolytic activity to activate membrane-interacting peptides, localizing cargos near the site of proteolysis. We demonstrate that RIPs can deliver diverse therapeutic cargos, including cytotoxins and radioisotopes. As proof of concept, we engineered “FRIP,” a RIP designed for cleavage by fibroblast activation protein (FAP), an endoprotease upregulated in solid tumors and fibrosis. Efficient P4–P4’ substrate sequences were identified and incorporated into FRIPs. Cell-based studies showed that, upon activation, the peptide adhered to membranes rapidly internalized and successfully delivered therapeutic cargos. Consistent with this, FRIPs delivering MMAE inhibited proliferation in an FAP-dependent manner. Imaging studies confirmed tumor targeting with minimal uptake in normal tissues. Finally, FRIPs delivering MMAE or Cu-67 exhibited potent antitumor effects. These findings establish membrane tethering as a strategy to enhance drug retention.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Building High-Energy Silicon-Containing Batteries Using Off-The-Shelf Materials

The technology of silicon anodes appears to be reaching maturity, with high-energy Si cells already in pilot-scale production. However, the performance of these systems can be difficult to replicate in academic settings, making it challenging to translate research findings into solutions that can be implemented by the battery industry. Part of this difficulty arises from the lack of access to engineered Si particles and anodes, as electrode formulations and the materials themselves have become valuable intellectual property for emerging companies. Here, we summarize the efforts by Argonne’s Cell Analysis, Modeling, and Prototyping (CAMP) Facility in developing Si-based prototypes made entirely from commercially available materials. We describe the many challenges we encountered when testing high-loading electrodes (>5 mAh cm −2 ) and discuss strategies to mitigate them. With the right electrode and electrolyte design, we show that our pouch cells containing ≥ 70 wt% SiO x can achieve 600–1,000 cycles at C/3 and meet projected energy targets of 700 Wh L −1 and 350 Wh kg −1 . These results provide a practical reference for research teams seeking to advance silicon-anode development using accessible materials.

25 ENERGY STORAGE↗
DOE OSTI2025

Broken symmetries associated with a Kagome chiral charge order

Chirality, or handedness, is ubiquitous in science, from cell biology to physics, and in condensed matter can underlie exotic phases such as chiral charge density waves and chiral superconductivity. However, detecting subtle broken symmetries that define such states is challenging, leading to debate and controversy. Here, using second-order optical response, we reveal the broken symmetries of a chiral charge density wave in the Kagome lattice KV 3 Sb 5 . Polarization-dependent mid-infrared photocurrent microscopy uncovers a longitudinal, helicity-dependent photocurrent associated with the charge order, indicating broken inversion and mirror symmetries. These findings, supported by theoretical analysis, directly establish the intrinsic chiral nature of the ordered state. Moreover, the absence of a circular photogalvanic effect perpendicular to the incident light imposes stringent constraints on the point-group symmetries. Our study not only visualizes the chiral nature of the Kagome charge order, but also highlights the nonlinear photogalvanic effect as a sensitive probe for detecting subtle symmetry breakings.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Protocol to detect dilution cycles in chemostat experiments and estimate growth rate slopes with linear modeling with R software chemostat_regression

Chemostat growth chambers measure optical density over time and require manual calculation of growth rates. Here, we present chemostat_regression, R software that enables users to automatically identify chemostat cycles and estimate growth rate using a linear regression approach. We describe steps for creating requisite software environment(s), formatting input data, executing the software via command line/RStudio/R-Shiny, interpreting results, assessing the validity of results, and modifying input parameters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mechanical Roles of Polysaccharide Assembly and Interactions in Plant Cell Walls

Plants synthesize polysaccharide-based primary cell walls that possess unique microstructures and mechanical properties to accommodate plant growth and provide protection. Here, it remains challenging to assess the role of polysaccharide organization and interactions in the mechanical behavior of primary cell walls owing to their complex microstructure and highly nonlinear mechanical responses. Employing a coarse-grained molecular dynamics model developed for onion epidermal walls, this work explores the conditions under which polysaccharide assembly and interactions might play a significant role in primary cell wall mechanics. Cellulose–cellulose adhesion plays a dominant role in the wall load-bearing capacity, but when cellulose–cellulose adhesion was disrupted computationally, cellulose–xyloglucan adhesion could influence the wall load-bearing capacity. Contrary to the common concept that xyloglucans mechanically tether well-separated cellulose microfibrils, xyloglucans functioned in this case as interfibrillar adhesives capable of transmitting tensile forces between cellulose microfibrils. Our findings may inform design criteria of new materials inspired by plant cell walls.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis

The polymorphic membrane proteins (Pmps) are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, which correspond to the coils of a large beta-helical domain in high quality structure predictions. Analysis of the protein using structure prediction algorithms provided novel insight to the chlamydial Pmp family of proteins. While the tetrapeptide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself. This analysis more accurately defines the Pmp family of Chlamydia and may better inform rational vaccine design and functional studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Design-driven optimization of low-cost reagent formulations for reproducible and high-yielding cell-free gene expression

Access to recombinant proteins is vital in basic science and biotechnology research. Cell-free gene expression systems provide one approach to address this need, but widespread utilization remains limited by the cost, complexity, and inconsistency of current platforms. To address these limitations, we carry out a multi-dimensional definitive screening design to reduce the number of reagent components and remove costly secondary energy substrates. From 1,231 different reagent formulations, we discover a simple and reproducible system based on 12 components. The optimized reagent formulation can produce 2.4 ± 0.3 g/L of protein product at the 15-µL scale (~$\$60$/gprotein) and 3.7 ± 0.2 g/L (~$\$39$/gprotein) at the 4-mL scale with oxygen supplementation. This provides an average 95% reduction in cost over previous cell-free reagent formulations. We further show that the optimized reagent formulation can produce nucleoside triphosphates from nitrogenous bases and ribose and that it is robust to failure across batches of cell lysates, users/locations, and in the synthesis of more than 20 different proteins. For example, we demonstrate the production of fifteen therapeutically relevant products, including full-length aglycosylated monoclonal antibodies. We anticipate that our optimized reagent formulation will democratize the use of cell-free systems for protein manufacturing and synthetic biology applications.

Biologics↗
DOE OSTI2024

The Maintainable Fusion Pilot Plant

The US fusion community has coalesced around the goal of building an FPP as described by the National Academies of Science, Engineering, and Medicine (NASEM). In addition to demonstrating the viability of the technologies necessary to operate such a plant, including demonstration of net energy and electricity production, NASEM found that a “fusion pilot plant will need to demonstrate the ability to efficiently perform remote maintenance and replacement in support of the design of a power plant, taking into account details of the consequences of the fusion environment, such as material activation and tritium retention in components.” Current designs of fusion demonstration reactors do usually foresee a regular exchange of their first wall modules, including the tritium breeding blankets. In the European Power Plant Conceptual Studies, it is assumed that a fusion reactor will need to change its divertor every 2 years and its first wall blanket module every 5 to 6 years to reach acceptable availability. Underlying this capability are remote-handling technologies to keep the outage for the exchange of these components short. There are many uncertainties in the remote-handling schemes, and most schemes are at a preconceptual level at best. In addition, the exchange of these components would either produce an enormous rad-waste stream or would require an enormous refurbishment activity with huge cost-prohibitive hot-cells. Past Fusion Nuclear Science Facility (FNSF) preconceptual studies have led to hot cell dimensions of an unbelievable size, likely costing tens of billions of dollars. Already at The Way (previously International Thermonuclear Experimental Reactor, ITER), hot-cells have become cost-prohibitive, demanding redesigns of the ITER first wall to reduce the toxic rad-waste/inventory. In this in-situ PFC repair project, a concept for a long-life, maintainable first wall module concept is developed and tested. This first wall concept relies on innovative remote handling to repair the first wall modules in-situ, avoiding costly refurbishments outside of the tokamak vessel. This approach was highlighted in the Fusion Energy Sciences Advisory Committee (FESAC) report on Transformative Enabling Capabilities for Efficient Advance Toward Fusion Energy. In general, the damage of the first wall armor is due to particle and radiation exposures. Load conditions vary from one fusion reactor design to another. In tokamaks, first wall Plasma Facing Components (PFCs) are exposed to far-Scrape-Off-Layer plasma fluxes, electromagnetic radiation, energetic CX neutrals, and potentially runaway electron beams. Protecting the first wall to the worst-case load conditions would require the design of a very thick first wall armor. Transient heat and particle fluxes due to disruptions or edge localized modes can lead to excessive heat loads resulting potentially in melting PFCs down to the cooling channel. Catastrophic events like these need to be avoided by appropriate disruption mitigation systems. However, failure of these systems will still put a first wall at an unacceptable risk. Hence, a first wall design needs to accommodate the occasional transient heat loads by introducing sacrificial limiters, which will absorb these transients.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗