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804 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Editorial: Nanotechnology for natural products

Humans around the globe have lived through an unprecedented time. The emergence and rapid spread of coronavirus disease 2019 (COVID-19) have resulted in the loss of millions of lives, and this number is still climbing every day and hour. As a consequence, there have been drastic changes over the past two years in how we live, communicate, and work, some of which may have changed forever: remote conferencing has become a new norm for businesses, schools, and academia; work-from-home and hybrid working is now more than just acceptable in many industries; most importantly, COVID-19 has raised global awareness of infectious diseases and pandemic responses to an exceptional level. Certainly, COVID-19 is not the only disease that is causing human suffering at this moment. Other highly contagious and lethal viruses, such as the human immunodeficiency virus (HIV), Ebola, and the recent addition to the list, Monkeypox, pose extraordinary challenges to modern civilizations. On the other hand, non-communicable diseases, such as heart disease, stroke, and cancer, are still claiming the majority of deaths on a global level (World Health Organization, 2020). Before the availability of synthetic drugs, civilizations worldwide relied on natural products extracted from the environment and various organisms for healthcare. Natural products and their derivatives continue to be critical components in the drug library available today. Indeed, almost a quarter of the new drugs approved by the US Food and Drug Administration (FDA) since 1981 are natural products, botanical mixtures, or their derivatives (Newman and Cragg, 2020). Recent developments in analytical characterization, genome mining, and engineering have further increased interest in drug discovery from the pool of natural products (Atanasov et al., 2021). This Research Topic celebrates a collection of studies at the intersection of natural product research and nanotechnological advances. As a successor and extension of the Research Topic in “Nanotechnology in Traditional Medicines and Natural Products” published last year (Zhang et al., 2021), the present collection focused more on recent developments in employing the synthesis and characterization of nanostructures for the delivery of functional natural products. Specifically, the use of carrier nanostructures to conjugate or encapsulate therapeutically active natural products with carrier nanostructures could enable their robust, targeted delivery tailored to either tackle a specific disease or unlock a drug administration pathway. Over the last decade, nanostructures such as liposomes (Pattni et al., 2015) and lipid nanoparticles (Hou et al., 2021) have been developed as versatile platforms for the inclusion and delivery of a wide range of therapeutical compounds; a significant advance in this aspect is the stabilization of mRNA strands for COVID-19 vaccination recently produced by Pfizer/BioNTech and Moderna (Tenchov et al., 2021). Such engineered nanomaterials are now widely used in the development of new drugs, while regulatory forces, such as the US FDA, remain cautious with the evaluation of each product on a case-by-case basis (Wang and Grainger, 2022). In this collection, Zeng et al. provided a timely review of natural products conjugated to and contained within nanomaterials for the ongoing COVID-19 pandemic. Natural products that are potentially useful in the mitigation of this disease, such as chloroquine and curcumin, supported in nanocarrier systems, have been discussed in detail. More broadly, Cheng et al. comprehensively reviewed the use of liposomes as a nanocarrier for natural products. This article provides a summary of natural product compounds and extracts used to form liposomal structures. Readers can further enjoy the practical aspects of these engineered drugs for the treatment of specific diseases as well as insights into future directions in this field.

peptides↗
DOE OSTI2025

FAIR to WISE (F2W) v1.0.0

FAIR to WISE (F2W) is an iterative, large-language model (LLM) driven pipeline that turns unstructured research PDFs into structured, queryable knowledge graphs (KGs). Core features include schema-driven extraction to a LinkML model; full provenance capture; ontology-grounded enrichment (e.g., chemical validation and ChEBI lookup); graph construction to JSON-LD with stable IDs; and KG-RAG question answering with evidence-aware retrieval. The system is engineered for reproducibility and accessibility (open-source Ollama models, temperature=0, NVTX/Nsight profiling) with robust QA (relation verification, deduplication, and deterministic outputs). Primary uses are literature-to-KG automation, knowledge-grounded Q&A, and experimental steering support. We demonstrate the approach in organic photovoltaics, where the pipeline ingests papers, builds a domain KG, and evaluates answers against expert competency questions to guide experimental planning and interpretation. Compared with off-the-shelf LLMs and ad-hoc NLP tools, F2W addresses ontology gaps and reduces hallucination risk by grounding responses in extracted evidence and enforcing schema constraints; it also offers deterministic, provenance-linked outputs and open, cost-aware deployment. Evidence-aware ranking further improves answer quality over pure vector search.

Abramov, David [Lawrence Berkeley National Laborat↗
NASA NTRS1996

Sequence, overproduction and purification of Vibrio proteolyticus ribosomal protein L18 for in vitro and in vivo studies

A strategy suggested by comparative genomic studies was used to amplify the entire Vibrio proteolyticus (Vp) gene for ribosomal protein L18. Vp L18 and its flanking regions were sequenced and compared with the deduced amino acid (aa) sequences of other known L18 proteins. A 26-aa residue segment at the carboxy terminus contains many strongly conserved residues and may be critical for the L18 interaction with 5S rRNA. This approach should allow rapid characterization of L18 from large numbers of bacteria. Both Vp L18 and Escherichia coli (Ec) L18 were overproduced and purified using a T7 expression vector which fuses an N-terminal peptide segment (His-tag) containing 6 histidine residues to the recombinant protein. The purified fusion proteins, Vp His::L18 and Ec His::L18, were both found to bind to either the Vp 5S or Ec 5S rRNAs in vitro. Vp His::L18 protein was also shown to incorporate into Ec ribosomes in vivo. This His-tag strategy likely will have general applicability for the study of ribosomal proteins in vitro and in vivo.

Non-NASA Center↗
DOE OSTI2026

Data for Photoenzymatic Stereoablative Enantioconvergence of γ-chiral Oximes via Hydrogen Atom Transfer

Producing enantioenriched molecules from racemic mixtures is essential for manufacturing. Traditional methods such as resolution, deracemization and enantioconvergent catalysis primarily involve separating or converting enantiomers without altering their structures, or functionalization of stereocentres at or proximal to functional groups. However, there are challenges in enantioselectively forging C–H bonds that are remote from functional groups via hydrogen atom transfer (HAT) with these methods. Here we introduce a strategy for the photoenzymatic stereoablative enantioconvergence of γ-chiral oximes using repurposed flavin-dependent ene-reductases. A photoinduced single-electron reduction of the γ-chiral oxime by an ene-reductase generates an iminyl radical, which then undergoes stereoablative 1,5-HAT at the γ-stereocentre. Subsequent chiral reconstruction through enzymatic HAT and spontaneous imine hydrolysis yields the γ-chiral ketone with high enantioselectivity. This work provides a robust method for remote stereoablative enantioconvergent HAT and broadens the synthetic utility of photobiocatalysis.

Bioproducts↗
DOE OSTI2025

Structural basis of heme scavenging by the ChtA and HtaA hemophores in Corynebacterium diphtheriae

Corynebacterium diphtheriae causes diphtheria, a potentially fatal infectious disease that damages tissues in the upper respiratory tract. In order to proliferate, this pathogen acquires the essential nutrient iron from heme (iron-protoporphyrin IX) primarily found in human hemoglobin (Hb). C. diphtheriae secretes ChtA and HtaA hemophore proteins that bind ferric heme (hemin) via conserved region (CR) domains. Here, we demonstrate that their CR domains scavenge hemin after it is spontaneously released from Hb, and define the structural basis of hemin binding to ChtA and the N-terminal CR domain from HtaA by determining X-ray crystal structures of their protein-hemin complexes. Resonance Raman and electron paramagnetic resonance experiments demonstrate that the CR domains from ChtA and HtaA engage in pentacoordinate hemin binding through a conserved iron-tyrosyl linkage, though variations in their hemin pockets alter the way they stabilize the axial tyrosine and mask hemin’s metal. The importance of these interactions is probed using isothermal titration calorimetry experiments, which represent the first quantitative assessment of CR-hemin affinity and reveal that ChtA binds hemin via an enthalpically driven process. Hemin partitioning experiments using native mass spectrometry demonstrate that the cohort of CR domains within C. diphtheriae ’s hemin-uptake system have dissociation constants for hemin between 0.8 and 22 nM, raising the possibility that affinity differences contribute to the directional flow of hemin into the cell. Collectively, the results of this work provide insight into how C. diphtheriae and other pathogenic and commensal corynebacterium species utilize CR domains to scavenge iron rich hemin from their environment.

Corynebacterium diphtheriae↗
DOE OSTI2021

Understanding the dynamics of vacuole trafficking and secretion for enhanced plant storage reserves

Vacuoles are essential in plants and serve roles in both protein and organelle degradation for reutilization and storage of high energy molecules such as storage proteins which are critical for seed germination under normal and stress conditions and impact biomass production and nutrition. In addition, plants secrete many different molecules such as cell wall components, lipids, waxes and others that are important for plant protection, structure and biomass. Vacuole accumulation and secretion are closely linked and highly regulated pathways within the endomembrane trafficking network. We have discovered many drug-like synthetic small molecules that can suppress vacuole trafficking and enhance secretion; other chemicals can enhance vacuole trafficking and suppress secretion. The ability of our compounds to modulate these pathways indicates that these pathways are tightly coupled and highly regulated. Thus, to achieve the goals of enhanced energy reserves or enhanced secretion it is essential to understand how this dynamic is controlled. Bioactive chemicals have provided us unique insight into natural mechanisms controlling the dynamics of vacuole trafficking and secretion that was not possible previously. One such compound, ES2, negatively modulates secretion while enhancing vacuole trafficking. This is the first compound discovered that targets an essential secretory complex known as the exocyst and will reveal important regulatory domains controlling secretion and vacuole trafficking. During the current funding period, we determined the structure of the EXO70A1 in plants and identifying its binding site. To understand the dynamics of vacuole trafficking it is key to have compounds that inhibit vacuole trafficking as well as enhancing it (ES2). We have used sophisticated image analysis to identify another novel compound ES17 that enhances secretion while negatively modulating vacuole trafficking (opposite of ES2). We have already made rapid progress. Our preliminary data indicates that ES17 very specifically targets a late stage of vesicle fusion with the tonoplast which is highly regulated. Thus, ES17 is an ideal compound to dissect the regulation of vacuole targeting dynamics. In addition, we have now synthesized a biotinylated version of ES17 that is fully functional, permitting the use of chemical proteomics to identify the cognate target with a high probability of success. We propose to investigate the ES17 target which can negatively modulate vacuole trafficking and combine this with knowledge of the ES2 target which can promote vacuole trafficking. Dissecting the mechanisms controlling the dynamics of secretion vs vacuole accumulation and the use of synthetic modulators will permit us to understand and regulate trafficking to enhance secretion to the plasma membrane and cell wall or the accumulation of biological energy reserves for increased biomass, nutritional value, stress resistance, and the secretion of specialized plant products.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Structural characterization and regulatory element analysis of the heart isoform of cytochrome c oxidase VIa

In order to investigate the mechanism(s) governing the striated muscle-specific expression of cytochrome c oxidase VIaH we have characterized the murine gene and analyzed its transcriptional regulatory elements in skeletal myogenic cell lines. The gene is single copy, spans 689 base pairs (bp), and is comprised of three exons. The 5'-ends of transcripts from the gene are heterogeneous, but the most abundant transcript includes a 5'-untranslated region of 30 nucleotides. When fused to the luciferase reporter gene, the 3.5-kilobase 5'-flanking region of the gene directed the expression of the heterologous protein selectively in differentiated Sol8 cells and transgenic mice, recapitulating the pattern of expression of the endogenous gene. Deletion analysis identified a 300-bp fragment sufficient to direct the myotube-specific expression of luciferase in Sol8 cells. The region lacks an apparent TATA element, and sequence motifs predicted to bind NRF-1, NRF-2, ox-box, or PPAR factors known to regulate other nuclear genes encoding mitochondrial proteins are not evident. Mutational analysis, however, identified two cis-elements necessary for the high level expression of the reporter protein: a MEF2 consensus element at -90 to -81 bp and an E-box element at -147 to -142 bp. Additional E-box motifs at closely located positions were mutated without loss of transcriptional activity. The dependence of transcriptional activation of cytochrome c oxidase VIaH on cis-elements similar to those found in contractile protein genes suggests that the striated muscle-specific expression is coregulated by mechanisms that control the lineage-specific expression of several contractile and cytosolic proteins.

Non-NASA Center↗
DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗
DOE OSTI2026

Data for The Value of Reversible Carbon Storage in a Zero-Emissions World

Atmospheric carbon dioxide removal (CDR) is required to stabilize global temperature. CDR can be achieved via ecosystem-based approaches that are cost-effective but reversible (e.g., soil and forest management) or by more durable but expensive approaches (e.g., direct air capture coupled with geologic storage). Here, we examine trade-offs between these approaches, focusing on timing, climate impacts, and cost. We simulated reversible carbon accrual for a range of CDR contract structures using a general minimalist model of ecosystem carbon cycling, and parameterized it to simulate US agricultural soil management─specifically cover cropping─as a case study. We then quantified the resulting impact on atmospheric carbon and global temperature using a climate model emulator. We find that maintaining a patchwork of reversible CDR projects by replacing lapsed projects with new projects can reduce warming by 22–195 μ°C in 2100 and that the magnitude of this cooling effect depends on how effectively the patchwork is maintained. Long-term maintenance of reversible CDR projects requires institutional stability that cannot be guaranteed over multiple decades. Consequently, effective CDR ultimately requires replacing reversible projects with durable projects. To address this problem, we modeled the cost of replacing reversible agricultural soil CDR with geologic CDR. We found that using reversible CDR as a bridge to durable CDR is potentially more cost-effective as a global cooling strategy (0.20–0.81 billion USD per μ°C avoided) than perpetual maintenance of reversible CDR (0.32–1.31 billion USD per μ°C avoided) or an immediate transition to durable CDR (1.37–2.19 billion USD per μ°C avoided). However, we emphasize that institutional commitments to maintain reversible CDR projects cannot be guaranteed. Reliance on reversible CDR as a bridge to durable CDR therefore carries an unknown amount of risk and will only function if efforts to maintain reversible CDR are robust.

Carbon↗
DOE OSTI2025

CRISPR/Cas9 editing of p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE 1 in maize alters phenolic metabolism, lignin structure, and lignin-first biomass processing

Valorization of lignocellulosic biomass for sustainable production of high-value chemicals is challenged by the complexity of lignin, a phenolic biopolymer. Beyond the classical lignin monomers derived from p-coumaryl, coniferyl, and sinapyl alcohol, grass lignins incorporate substantial amounts of monolignol p-coumarates that are produced by p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE (PMT). Here, the CRISPR/Cas9-mediated mutation of ZmPMT1 in maize enabled the design of biomass depleted in p-coumaroylated lignin and enriched in guaiacyl lignin. Lignin-first biorefining of stem biomass from zmpmt1 mutants by reductive catalytic fractionation (RCF) generated a lignin oil depleted in carboxylates and enriched in guaiacyl-derived alcohols, which are desirable substrates for bio-based polyurethane synthesis. Furthermore, the reported lignin engineering in maize is a promising strategy for designing a dual-purpose crop, providing both food and feed, along with a renewable feedstock for the production of plant-based chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbiome dynamics in the congregate environment of U.S. Army Infantry training

Within military training and operational environments, individuals from diverse backgrounds share common spaces, follow structured routines and diets, and engage in physically demanding tasks. While there has been interest in leveraging microbiome features to predict and improve military health and performance, the longitudinal convergence of microbiomes in such constrained environments has not been established. To assess the degree of microbiome convergence, we performed shotgun metagenomic sequencing on swab samples from a military trainee cohort. Samples were taken across four different body sites, three timepoints, and two spatially distinct platoons. We observed evidence of convergence in one platoon, whereby similarity in microbiome composition increased over time, with numerous differentially abundant species. We found no indication of strain transfer between individuals, suggesting that convergence was influenced by external environmental factors, diet, and lifestyle. Microbial shifts observed in the convergence process included a decrease in fungal species, such as Malassezia restricta in nasal cavities, and a decrease in Prevotella species at inguinal regions across time. Shifts in multiple Corynebacterium species were also observed with varying magnitudes depending on the body site. Overall, we provide preliminary evidence of convergence of host microbial communities in military-associated environments that were distinguishable using shotgun metagenomic sequencing approaches. The data presented here on microbiome convergence, dynamics, and stability may inform risk-based mitigation in congregate military settings facilitating development of targeted microbial, dietary, or other interventions to optimize health and performance of military populations.

Biological and medical sciences↗
DOE OSTI2026

Data for Multisite Field Evaluation of Oil Accumulation and Agronomic Performance in Grain and Sweet Sorghums Engineered for Lipid Hyperaccumulation

Oil sorghum (OS) has been developed by engineering grain (TX430) and sweet (Ramada) genetic backgrounds to accumulate triacylglycerols (TAG) in vegetative tissues as an energy-dense feedstock for sustainable aviation fuel (SAF) and other biofuels. This study evaluated two TX430 OS lines (TxHO-2, TxHO-3) and two Ramada OS lines (RmHO-1, RmHO-2) alongside wild-type (WT) lines in NE and IL over 2 years (2023–2024) to quantify genotype × environment effects on agronomic performance and TAG accumulation. Across four environments, TX430 OS lines showed average TAG concentrations of 15.0 g kg−1 in leaves and 12.8 g kg−1 in stems, approximately 19-fold higher than WT. Ramada OS lines accumulated 26.1 g kg−1 in leaves and 12.3 g kg−1 in stems, approximately 25-fold and 13-fold increases over WT, respectively. OS lines in TX430 exhibited an 18% reduction in biomass (8.4 vs. 9.9 Mg ha−1 for WT), while Ramada OS lines had similar WT biomass (18.3 vs. 19.9 Mg ha−1 for WT). Among TX430 OS lines, TxHO-2 achieved the highest TAG yield (190 kg ha−1), while RmHO-1 led the Ramada lines (335 kg ha−1) due to higher biomass and similar TAG concentration. Enhanced TAG accumulation increased N, P, and K removal in TX430 lines but not in Ramada lines. Structural carbohydrate and ash concentration were unaffected. Overall, results confirm vegetative lipid accumulation as a viable strategy for high-biomass sorghum, supporting its potential as a dual-purpose feedstock for SAF. Future work should focus on minimizing biomass yield penalties and improving nutrient use efficiency in oil sorghum systems.

Agronomy↗