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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Bacterial Volatile Organic Compounds as a Strategy to Increase Drought Tolerance in Maize (Zea mays L.): Influence on Plant Biochemistry

Maize is highly susceptible to drought, which affects growth and yield. This study investigated how bacterial volatile organic compounds (BVOCs) affect maize drought tolerance. Drought reduced shoot size but increased root length, an adaptation for accessing deeper soil moisture. BVOCs from strain D12 significantly increased root length and shoot growth under drought conditions. Drought also altered root biochemistry, decreasing enzyme activity, and increased osmolyte levels. BVOCs from strains F11 and FS4-14 further increased osmolyte levels but did not protect membranes from oxidative damage, while BVOCs from strains D12 and D7 strains reduced osmolyte levels and cell damage. In shoots, drought increased the levels of osmolytes and oxidative stress markers. BVOCs from FS4-14 had minimal effects on shoot biochemistry. BVOCs from D12 and F11 partially restored metabolic activity but did not reduce cell damage. BVOCs from D7 reduced metabolic activity and cell damage. These results suggest that BVOCs can modulate the biochemical response of maize to drought, with some strains evidencing the potential to enhance drought tolerance.

Lopes, Tiago (ORCID:0000000330603315)↗
DOE OSTI2021

Kinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communities

Microbial organisms engage in a variety of metabolic interactions. A crucial part of these interactions is the exchange of molecules between different organelles, cells, and the environment. The main forces mediating this metabolic exchange are transporters. This transport can be difficult to measure experimentally because several transport mechanisms remain opaque. However, theoretical calculations about the inputs and outputs of cells via metabolic exchanges have enabled the successful inference of the workings of intra-organismal and inter-organismal systems. Kinetic, metabolic, and statistical modeling approaches in combination with omics data are enhancing our knowledge and understanding about metabolic exchange and mass resource allocation. Furthermore, this model-driven analytics approach can guide effective experimental design and yield new insights into biological function and control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Pharmacological Inhibition of HSP90 Radiosensitizes Head and Neck Squamous Cell Carcinoma Xenograft by Inhibition of DNA Damage Repair, Nucleotide Metabolism, and Radiation-Induced Tumor Vasculogenesis

Recent preclinical studies suggest combining the HSP90 inhibitor AT13387 (Onalespib) with radiation (IR) against colon cancer and head and neck squamous cell carcinoma (HNSCC). These studies emphasized that AT13387 downregulates HSP90 client proteins involved in oncogenic signaling and DNA repair mechanisms as major drivers of enhanced radiosensitivity. Given the large array of client proteins HSP90 directs, we hypothesized that other key proteins or signaling pathways may be inhibited by AT13387 and contribute to enhanced radiosensitivity. Metabolomic analysis of HSP90 inhibition by AT13387 was conducted to identify metabolic biomarkers of radiosensitization and whether modulations of key proteins were involved in IR-induced tumor vasculogenesis, a process involved in tumor recurrence.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Biocatalytic gateway to convert glycerol into 3-hydroxypropionic acid in waste-based biorefineries: Fundamentals, limitations, and potential research strategies

Microbial conversion of bioenergy-derived waste glycerol into value-added chemicals has emerged as an important bioprocessing technology due to its eco-friendliness, feasible technoeconomics, and potential to provide sustainability in biodiesel and bioethanol production. Glycerol is an abundant liquid waste from bioenergy plants with a projected volume of 6 million tons by 2025, accounting for about 10% of biodiesel and 2.5% of bioethanol yields. 3-Hydroxypropionic acid (3-HP) is a major product of glycerol bioconversion, which is the third largest biobased platform compound with expected market size and value of 3.6 million tons/year and USD 10 billion/year, respectively. Despite these biorefinery values, 3-HP biosynthesis from glycerol is still at an immature stage of commercial exploitation. The main challenges behind this immaturity are the toxic effects of 3-HPA on cells, the distribution of carbon flux to undesirable pathways, low tolerance of cells to glycerol and 3-HP, co-factor dependence of enzymes, low enzyme activity and stability, and the problems of substrate inhibition and specificity of enzymes. To address these challenges, it is necessary to understand the fundamentals of glycerol bioconversion and 3-HP production in terms of metabolic pathways, related enzymes, cell factories, midstream process configurations, and downstream 3-HP recovery, as discussed in this review critically and comprehensively. It is equally important to know the current challenges and limitations in 3-HP production, which are discussed in detail along with recent research efforts and remaining gaps. Finally, possible research strategies are outlined considering the recent technological advances in microbial biosynthesis, aiming to attract further research efforts to achieve a sustainable and industrially exploitable 3-HP production technology. Here, by discussing the use of advanced tools and strategies to overcome the existing challenges in 3-HP biosynthesis, this review will attract researchers from many other similar biosynthesis technologies and provide a common gateway for their further development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Integration of genome-scale metabolic model with biorefinery process model reveals market-competitive carbon-negative sustainable aviation fuel utilizing microbial cell mass lipids and biogenic CO 2

Producing scalable, economically viable, low-carbon biofuels or biochemicals hinges on more efficient bioconversion processes. While microbial conversion can offer robust solutions, the native microbial growth process often redirects a large fraction of carbon to CO 2 and cell mass. By integrating genome-scale metabolic models with techno-economic and life cycle assessment models, this study analyzes the effects of converting cell mass lipids to hydrocarbon fuels, and CO 2 to methanol on the facility’s costs and life-cycle carbon footprint. Results show that upgrading microbial lipids or both microbial lipids and CO 2 using renewable hydrogen produces carbon-negative bisabolene. Additionally, on-site electrolytic hydrogen production offers a supply of pure oxygen to use in place of air for bioconversion and fuel combustion in the boiler. To reach cost parity with conventional jet fuel, renewable hydrogen needs to be produced at less than $\$2.2$ to $\$3.1$/kg, with a bisabolene yield of 80% of the theoretical yield, along with cell mass and CO 2 yields of 22 wt% and 54 wt%, respectively. The economic combination of cell mass, CO 2 , and bisabolene yields demonstrated in this study provides practical insights for prioritizing research, selecting suitable hosts, and determining necessary engineered production levels.

09 BIOMASS FUELS↗
DOE OSTI2025

Editorial overview: Unlocking the secrets of nongenetic plasticity, one cell at a time

Cellular noise, the non-genetic variability observed among isogenic cells, arises from factors such as growth conditions, aging, and stochastic gene expression, influencing cell stress-response, metabolism, morphology, and size. Here, such plasticity, while critical for adaptation, often goes unnoticed with traditional population-averaging biotechnologies that inevitably mask cell-specific variations and prompting the question, "What else might we be missing". However, recent breakthroughs in optical imaging, microfluidics, and omics, are beginning to uncover the complexity of cellular plasticity. This special is-sue highlights some of these breakthroughs, with key contributions including innovations in multimodal chemical imaging, label-free microscopy, spatial and temporal omics, and droplet-based microfluidics. Collectively, these cutting-edge tools provide unprecedent-ed insights into non-genetic cell-to-cell variability, enhancing our understanding of cellu-lar plasticity and its implications for health, energy, and ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Conversion of S-lignin compounds to useful intermediates

The present disclosure relates to a genetically modified microbial cell that includes a genetic modification resulting in the expression of a vanillate demethylase, where the microbial cell is capable of metabolizing at least one S-lignin decomposition molecule including at least one of syringate and/or 3-O-methyl gallate, and the genetically modified microbial cell is capable of producing gallate. In some embodiments of the present disclosure, the vanillate demethylase may include VanAB.

Beckham, Gregg Tyler↗
DOE OSTI2021

Analysis of the Innovation Trend in Cell-Free Synthetic Biology

Cell-free synthetic biology is a maturing field that aims to assemble biomolecular reactions outside cells for compelling applications in drug discovery, metabolic engineering, biomanufacturing, diagnostics, and education. Cell-free systems have several key features. They circumvent mechanisms that have evolved to facilitate species survival, bypass limitations on molecular transport across the cell wall, enable high-yielding and rapid synthesis of proteins without creating recombinant cells, and provide high tolerance towards toxic substrates or products. Here, we analyze ~750 published patents and ~2000 peer-reviewed manuscripts in the field of cell-free systems. Three hallmarks emerged. First, we found that both patent filings and manuscript publications per year are significantly increasing (five-fold and 1.5-fold over the last decade, respectively). Second, we observed that the innovation landscape has changed. Patent applications were dominated by Japan in the early 2000s before shifting to China and the USA in recent years. Finally, we discovered an increasing prevalence of biotechnology companies using cell-free systems. Our analysis has broad implications on the future development of cell-free synthetic biology for commercial and industrial applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Reimport of carbon from cytosolic and vacuolar sugar pools into the Calvin–Benson cycle explains photosynthesis labeling anomalies

Significance Photosynthesis metabolites are quickly labeled when 13 CO 2 is fed to leaves, but the time course of labeling reveals additional contributing processes involved in the metabolic dynamics of photosynthesis. The existence of three such processes is demonstrated, and a metabolic flux model is developed to explore and characterize them. The model is consistent with a slow return of carbon from cytosolic and vacuolar sugars into the Calvin–Benson cycle through the oxidative pentose phosphate pathway. Our results provide insight into how carbon assimilation is integrated into the metabolic network of photosynthetic cells with implications for global carbon fluxes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism

Syntrophic microbial consortia can contribute significantly to the activity and function of anoxic ecosystems, yet are often too rare to study their in situ physiologies using traditional molecular methods. Here, in this study, we describe a technical innovation combining bioorthogonal non-canonical amino acid tagging (BONCAT), stable isotope probing, and metaproteomics to improve the recovery of proteins from active community members and track isotope incorporation. Both click chemistry-enabled cell-sorting and direct protein pulldown coupled to metaproteomics improved recovery of isotopically labeled proteins during acetate oxidation within a full-scale anaerobic digester. Resulting labeled protein expression profiles revealed elevated activity of a rare and uncharacterized syntrophic bacterium belonging to the family Natronincolaceae. BONCAT-based capture of newly translated proteins provided direct molecular evidence for the expression of a previously hypothesized oxidative glycine pathway for syntrophic acetate oxidation by this microorganism, showcasing the potential of targeted metaproteomics to characterize rare and active cells central to community metabolism in natural and engineered ecosystems.

Friedline, Skyler [Univ. of British Columbia, Vanc↗
DOE OSTI2023

Mass Spectral Imaging to Map Plant–Microbe Interactions

Plant–microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impact of sunitinib resistance on clear cell renal cell carcinoma therapeutic sensitivity in vitro

Sunitinib resistance creates a major clinical challenge for the treatment of advanced clear cell renal cell carcinoma (ccRCC) and functional and metabolic changes linked to sunitinib resistance are not fully understood. We sought to characterize the molecular and metabolic changes induced by the development of sunitinib resistance in ccRCC by developing and characterizing two human ccRCC cell lines resistant to sunitinib. Consistent with the literature, sunitinib-resistant ccRCC cell lines presented an aberrant overexpression of Axl and PD-L1, as well as a metabolic rewiring characterized by enhanced OXPHOS and glutamine metabolism. Therapeutic challenges of sunitinib-resistant ccRCC cell lines in vitro using small molecule inhibitors targeting Axl, AMPK and p38, as well as using PD-L1 blocking therapeutic antibodies, showed limited CTL-mediated cytotoxicity in a co-culture model. However, the AMPK activator metformin appears to sensitize the effect of PD-L1 blocking therapeutic antibodies and to enhance CTLs’ cytotoxic effects on ccRCC cells. These effects were not broadly observed with the Axl and the p38 inhibitors. Taken together, these data suggest that targeting certain pathways aberrantly activated by sunitinib resistance such as the AMPK/PDL1 axis might sensitize ccRCC to immunotherapies as a second-line therapeutic approach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

09 BIOMASS FUELS↗
DOE OSTI2024

The stem cell-type transcriptome of bioenergy sorghum reveals the spatial regulation of secondary cell wall networks

Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type.

cell specificity↗
DOE OSTI2026

Robust Rapid Cellular Metabolite Sensing Using Benchtop NMR and SABRE-Hyperpolarized [1- 13 C]Pyruvate

Hyperpolarized NMR has emerged as a powerful analytical technique to significantly enhance targeted NMR signals, improving the sensitivity for investigations of unique chemical and biological dynamics. Here, we demonstrate the use of a hyperpolarization strategy based on Signal Amplification By Reversible Exchange (SABRE) to generate highly reproducible doses of a hyperpolarized [1- 13 C]pyruvate probe for benchtop characterization of yeast metabolism. This method allows rapid, scalable, and benchtop preparation of biocompatible hyperpolarized solutions suitable for live-cell experiments. We show that this production can be dove-tailed into a modular, compact workflow to characterize real-time metabolism in cell cultures, using Saccharomyces cerevisiae (Baker’s yeast) as a model organism. With high temporal resolution, we show that this method can resolve the conversion of hyperpolarized [1- 13 C]pyruvate into oxidative decarboxylation products CO 2 and bicarbonate. This conversion exhibits sustained and detectable metabolic activity for over 300 s after introduction of the agent to the cells. We model the metabolite kinetics to show decarboxylation activity and derive estimates of the pH over time from the CO 2 and bicarbonate (carbonic acid buffer system) equilibrium to probe changes in the cellular environment during active metabolism. These results highlight the utility of benchtop SABRE-hyperpolarized [1- 13 C]pyruvate as a scalable, specific probe for metabolic phenotyping of living cells using compact, low-cost instrumentation well-suited for future high-throughput applications across microbial engineering, drug response profiling, and dynamic metabolic screening.

fungi↗
DOE OSTI2022

Regulation of Translation by Lysine Acetylation in Escherichia coli

Numerous cellular processes are regulated in response to the metabolic state of the cell. One such regulatory mechanism involves lysine acetylation, a covalent modification involving the transfer of an acetyl group from central metabolite acetyl-coenzyme A or acetyl phosphate to a lysine residue in a protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Engineering 2‐Pyrone‐4,6‐Dicarboxylic Acid Production Reveals Metabolic Plasticity of Poplar

Woody biomass is a promising source of fermentable sugars for biofuels and bio-based chemicals, but its industrial use is limited by the costly biorefinery process. A viable strategy to reduce costs involves enhancing both biomass processability and the generation of high-value co-products. Here, we report the implementation of a synthetic metabolic pathway in Populus tremula × P. alba to produce 2-pyrone-4,6-dicarboxylic acid (PDC), a key building block for biodegradable plastics and high-performance materials. This artificial pathway—comprising microbial genes AroG, QsuB, PmdA, PmdB, and PmdC—enabled de novo PDC production in the stems of transgenic poplar. Pathway expression also induced substantial metabolic reprogramming and altered cell wall composition. These include the hyperaccumulation of simple phenolics like protocatechuic acid (PCA) and vanillic acid (VA), alongside reduced levels of p-hydroxybenzoic acid. A large portion of VA was ester-linked to cell wall lignin, while PCA was incorporated into the lignin backbone, forming novel benzodioxane units; concurrently, lignin in transgenic plants exhibited a drastic reduction in guaiacyl- and syringyl-units, with a notable increase in p-hydroxyphenyl-units. Hemicellulose content, particularly xylan, was also significantly increased. Moreover, expression of the PDC-pathway led to the formation of novel VA-derived suberin aromatics, enhancing suberization in bark and roots and improving salt stress tolerance. These changes led to improved saccharification efficiency, with up to 25% more glucose and 2.5 times xylose released from woody biomass. These results demonstrate the metabolic flexibility of poplar and highlight its potential for engineering cost-effective, stress-resilient bioenergy crops with enhanced biorefinery traits.

2-pyrone-4↗