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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 1,153 records · Page 64
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NASA NTRS2012

Plant Science in Reduced Gravity: Lessons Learned

The effect of gravity on the growth and development of plants has been the subject of scientific investigation for over a century. The results obtained in space to test specific hypotheses on gravitropism, gene expression, seed formation, or growth rate are affected by both the primary effect of the microgravity and secondary effects of the spaceflight environment. The secondary effects of the spaceflight environment include physical effects arising from physical changes, such as the absence of buoyancy driven convective mixing, altered behavior of liquids and gases, and the environmental conditions in the spacecraft atmosphere. Thus, the design of biological experiments (e.g. cells, plants, animals, etc.) conducted in microgravity must account for changes in the physical forces, as well as the environmental conditions, imposed by the specific spaceflight vehicle and experimental hardware. In addition, researchers must become familiar with other aspects of spaceflight experiments: payload integration with hardware developers, safety documentation and crew procedures, and the logistics of conducting flight and ground controls. This report reviews the physical and environmental factors that directly and indirectly affect the results of plant science experiments in microgravity and is intended to serve as a guide in the design and implementation plant experiments in space.

Stutte, Gary W.↗
DOE OSTI2022

Tandem chemocatalysis and biological funneling to valorize lignin

In 2014, Linger et al. presented a tandem process for lignin valorization by integrating chemical and biological catalysis. Chemical pretreatment of corn stover generated mixed lignocellulose-derived monomers that were converted to a single product, polyhydroxyalkanoates, by Pseudomonas putida. Tandem processes have since been developed for diverse feedstocks to support the bioeconomy.

09 BIOMASS FUELS↗
DOE OSTI2020

Identification of a Na + -Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II

The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions, and one redox-inactive Ca 2+ ion, with two nearby bound Cl – ions. Sodium is a common counter-ion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Furthermore, we find that the oxygen-evolution activity of spinach PSII increases with [Na + ], particularly at high pH. A Na + -specific binding site next to the OEC, upon deprotonation of the D1-H337 amino-acid residue, is suggested by the analysis of two recently published PSII cryo-EM maps in combination with quantum mechanical calculations and molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

$\mathscr{PT}$ symmetry enforced twin exchange as the origin of chirality-induced spin selectivity

Chiral molecules, ubiquitous in chemistry and biology, can differentiate electrons by their spin, a phenomenon known as chirality-induced spin selectivity (CISS). Despite its robustness and technological relevance, CISS has resisted conventional explanation: Spin-orbit coupling (SOC) models cannot fully account for the observed magnitude, room-temperature persistence, or equilibrium signatures. Here, we argue that structural chirality enforces a twin-pair exchange mechanism via the indistinguishability principle, which intrinsically couples spin and spatial degrees of freedom such that wave functions cannot be factorized into spin and spatial components. We derive an effective Hamiltonian that describes both transport and equilibrium CISS phenomena and is non-Hermitian. However, the inherent pseudo-Hermiticity, with $\mathscr{PT}$ symmetry as a special case, ensures real eigenvalues and thermodynamic consistency. We demonstrate that our framework is a step toward resolving long-standing anomalies of CISS. It situates CISS alongside equilibrium symmetry-breaking phenomena such as ferromagnetism and superconductivity, with implications for spintronics, catalysis, and the origins of biological homochirality.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Cell-based composite materials with programmed structures and functions

The present invention is directed to the use of silicic acid to transform biological materials, including cellular architecture into inorganic materials to provide biocomposites (nanomaterials) with stabilized structure and function. In the present invention, there has been discovered a means to stabilize the structure and function of biological materials, including cells, biomolecules, peptides, proteins (especially including enzymes), lipids, lipid vesicles, polysaccharides, cytoskeletal filaments, tissue and organs with silicic acid such that these materials may be used as biocomposites. In many instances, these materials retain their original biological activity and may be used in harsh conditions which would otherwise destroy the integrity of the biological material. In certain instances, these biomaterials may be storage stable for long periods of time and reconstituted after storage to return the biological material back to its original form. In addition, by exposing an entire cell to form CSCs, the CSCs may function to provide a unique system to study enzymes or a cascade of enzymes which are otherwise unavailable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for α‐Diazoester Production

Abstract Azaserine is a bacterial metabolite containing a biologically unusual and synthetically enabling α‐diazoester functional group. Herein, we report the discovery of the azaserine ( aza ) biosynthetic gene cluster from Glycomyces harbinensis . Discovery of related gene clusters reveals previously unappreciated azaserine producers, and heterologous expression of the aza gene cluster confirms its role in azaserine assembly. Notably, this gene cluster encodes homologues of hydrazonoacetic acid (HYAA)‐producing enzymes, implicating HYAA in α‐diazoester biosynthesis. Isotope feeding and biochemical experiments support this hypothesis. These discoveries indicate that a 2‐electron oxidation of a hydrazonoacetyl intermediate is required for α‐diazoester formation, constituting a distinct logic for diazo biosynthesis. Uncovering this biological route for α‐diazoester synthesis now enables the production of a highly versatile carbene precursor in cells, facilitating approaches for engineering complete carbene‐mediated biosynthetic transformations in vivo.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement**

Abstract Histone deacetylases (HDACs) are important epigenetic regulators involved in many diseases, especially cancer. Five HDAC inhibitors have been approved for anticancer therapy and many are in clinical trials. Among the 11 zinc‐dependent HDACs, HDAC10 has received relatively little attention by drug discovery campaigns, despite its involvement, e. g., in the pathogenesis of neuroblastoma. This is due in part to a lack of robust enzymatic conversion assays. In contrast to the protein lysine deacetylase and deacylase activity of most other HDAC subtypes, it has recently been shown that HDAC10 has strong preferences for deacetylation of oligoamine substrates like acetyl‐putrescine or ‐spermidine. Hence, it is also termed a polyamine deacetylase (PDAC). Here, we present the first fluorescent enzymatic conversion assay for HDAC10 using an aminocoumarin‐labelled acetyl‐spermidine derivative to measure its PDAC activity, which is suitable for high‐throughput screening. Using this assay, we identified potent inhibitors of HDAC10‐mediated spermidine deacetylation in vitro. Based on the oligoamine preference of HDAC10, we also designed inhibitors with a basic moiety in appropriate distance to the zinc binding hydroxamate that showed potent inhibition of HDAC10 with high selectivity, and we solved a HDAC10‐inhibitor structure using X‐ray crystallography. We could demonstrate selective cellular target engagement for HDAC10 but a lysosomal phenotype in neuroblastoma cells that was previously associated with HDAC10 inhibition was not observed. Thus, we have developed new chemical probes for HDAC10 that allow further clarification of the biological role of this enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Integrating biocatalysis with chemocatalysis for selective transformations

The integration of biocatalysis with chemocatalysis combines the excellent selectivity of the former with the robust reactivity of the latter and offers many advantages, such as lower cost, higher yield, enhanced selectivity, as well as less waste generation. Despite the challenge of incompatibilities between different classes of catalysts, recent advances in synthetic chemistry and biology provide ample opportunities for multistep cascade transformations that combine biocatalysis and chemocatalysis. In this research, we review recent progress in merging biocatalysis with chemocatalysis, highlighting selected examples of photo-/electricity-driven biotransformations and recently developed strategies for addressing the catalyst incompatibility issue.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Modification of cell wall polysaccharide guides cell division in Streptococcus mutans

In ovoid-shaped, Gram-positive bacteria, MapZ guides FtsZ-ring positioning at cell equators. The cell wall of the ovococcus Streptococcus mutans contains peptidoglycan decorated with serotype c carbohydrates (SCCs). In the present study, we identify the major cell separation autolysin AtlA as an SCC-binding protein. AtlA binding to SCC is attenuated by the glycerol phosphate (GroP) modification. Using fluorescently labeled AtlA constructs, we mapped SCC distribution on the streptococcal surface, revealing enrichment of GroP-deficient immature SCCs at the cell poles and equators. The immature SCCs co-localize with MapZ at the equatorial rings throughout the cell cycle. In GroP-deficient mutants, AtlA is mislocalized, resulting in dysregulated cellular autolysis. These mutants display morphological abnormalities associated with MapZ mislocalization, leading to FtsZ-ring misplacement. Altogether, our data support a model in which maturation of a cell wall polysaccharide provides the molecular cues for the recruitment of cell division machinery, ensuring proper daughter cell separation and FtsZ-ring positioning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI

Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein–DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) (Final Scientific/Technical Report, Subcontract Award No. 6953691)

The overarching objective the Baliga lab is to develop a mechanistic understanding of the field relevant metabolic processes underlying community partitioning of respiration pathways and physiological state shifts. In order to dissect how environmental perturbations influence microbial regulatory networks, we have constructed data-driven models that capture the dynamic interplay between abiotic and biotic factors during laboratory simulations. Specifically, we have developed multiple computational models (i.e., cMonkey2, EGRIN 2.0, and multiple genome-scale metabolic models) connecting environmental influence to genome-encoded regulatory programs. In addition, we have generated new tools such as Live Anaerobic Cell Sorting (LAnCS) and Fluidized Bed Reactors (FBRs) to investigate the dynamics of community partitioning of metabolic processes supporting sulfate or nitrate respiration, which are two critical activities observed from the field site at Oak Ridge National Labs (ORNL). This framework of connecting field phenomena with laboratory simulations and computational modeling has created the Environmental Simulations and Modelling (EnvSim) campaign within ENIGMA. The campaign, which spans multiple laboratories across ENIGMA and is led by the Baliga group, has established synthetic communities (SynComs) to discover, characterize, and dissect key microbial processes relevant to field observations, such as emissions of the greenhouse gas nitrous oxide (N 2 O). For example, the EnvSim campaign so far has deduced four potential mechanisms that may account for the N 2 O emissions at the FRC and are currently being investigated by labs across ENIGMA. Denitrification may be driven by complete denitrifiers, however, their NosZ enzymes, which catalyze the final step in denitrification by converting N 2 O to N 2 , may be sensitive at a lower pH. Additionally, the denitrification process could be partitioned among organisms and some may have pH-sensitive NosZ genes. Another factor contributing to variable N 2 O emissions relates to the metal co-factors involved in the denitrification pathway. For instance, excess Cu, Al, Mn, U, Ni, Co, Cu, and/or Cd may have inhibitory effects on multiple enzymatic steps during denitrification, while the enzymatic production of nitrite, the precursor of N 2 O, can be limited by the essential metal Mo. Lastly, abiotic production of N 2 O may occur as a result of chemodenitrification, in which metals like Fe, Mn, and some organic compounds can drive redox reactions that convert nitrogen cycle intermediates to N 2 O under the right conditions. Current investigations and analyses have generated multiple transcriptomic profiles aiding the refinement of new metabolic and gene regulatory network model for our denitrifying SynCom. In sum, the previous funding cycle has generated 33 peer-reviewed publications spanning predictive network biology to co-operativity of mutualistic interspecies interactions of evolved communities. Our integration of multiple omics datasets and the development of new network modelling tools has revealed important insights that can explain field observed phenomenon and generated new hypotheses to be investigated in the field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1966

Biology and the Exploration of Mars

Until recent years the origin of life and its possible occurrence elsewhere in the universe have been matters for speculation only. The rapid growth of molecular biology since 1940 has, to be sure, made it possible to discuss life's origins in far more precise and explicit terms than was possible earlier; and the subject entered a new experimental phase in the 1950's with successful abiogenic synthesis of important biochemical substances in conditions simulating the presumptive environment of the primitive Earth. But the real transformation that the subject has undergone stems from the spectacular growth of space technology in the last decade. The possibility of life's origin and occurrence on planets other than ours is no longer limited to idle speculation: it has entered the realm of the testable, of science in the strict sense. Given the rockets now available, and especially those available by 1969, it has become fully realistic to consider plans for the biological exploration of Mars. The study that this report seeks to interpret was initiated in June, 1964, by the Space Science Board of the National Academy of Sciences to examine this possibility. The working group comprised 36 people representing a broad spectrum of scientific interests: evolutionary biology, genetics, microbiology, biochemistry and molecular biology, animal physiology, soil chemistry, organic chemistry, planetary astronomy, geochemistry, and theoretical physics. The participants included some with considerable prior involvement in problems of space exploration and others with none. Advice was also sought outside the group of immediate participants on the potentialities of selected analytical methods for the experimental study of extraterrestrial life and its environment. More than 30 individuals contributed in this fashion written assessments of techniques in which they were particularly well versed. Our task was to examine the scientific foundations and merits of the proposal to undertake a biological exploration of Mars. What are the potential scientific yields? How valuable, if attained, would they be? What, in fact, is the possibility of life occurring on Mars? And of our detecting it with available and foreseeable technology? What could be achieved by further astronomical work from Earth? by Martian fly-by missions? by Martian orbiters? and Martian Landers? What payloads would we recommend for planetary missions? What timing and over-all strategy would we recommend for Martian exploration were we to consider it worthwhile at all? In brief, the over-all purpose was to recommend to. the government, through the Academy's Space Science Board, whether or not a biological exploration of Mars should be included in the nation's space program over the next few decades; and, further, to outline what that program, if any, should be.

CONFERENCE↗
DOE OSTI2022

Extracellular vesicles in β cell biology: Role of lipids in vesicle biogenesis, cargo, and intercellular signaling

Background: Type 1 diabetes (T1D) is a complex autoimmune disorder whose pathogenesis involves an intricate interplay between ß cells of the pancreatic islet, other islet cells, and cells of the immune system. Direct intercellular communication within the islet occurs via cell surface proteins and indirect intercellular communication has traditionally been as occurring via secreted proteins (e.g., endocrine hormones and cytokines). However, recent literature suggests that extracellular vesicles (EVs) secreted by ß cells constitute an additional and biologically important mechanism for transmitting signals to adjacent ß cells or immune cells. Scope of Review: This review summarizes the general mechanisms of EV formation, with a particular focus on how lipids and lipid signaling pathways influence their formation and cargo. We review the implications of EV release from ß cells for T1D pathogenesis, how EVs and their cargo might be leveraged as biomarkers of the early events leading to T1D, and how EVs might be engineered as a therapeutic candidate to counter T1D outcomes. Major Conclusions: Islet ß cells have been viewed as initiators and propagators of the cellular circuit giving rise to autoimmunity in T1D. In this context, emerging literature suggests that EVs may represent a conduit for communication that holds more comprehensive messaging about the ß cells from which they arise. As the field of EV biology advances, it opens the possibility that intervening with EV formation and cargo loading could be a novel disease-modifying approach in T1D.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Enhancing organic matter removal, product recovery, and hydrogen generation from fermentation wastewater

Existing ethanol biorefineries produce billions of gallons of wastewater (stillage) that must be treated extensively prior to discharge or concentrated in an energy intense evaporation step to produce animal feed as a value-added bioproduct. Yeasts and filamentous fungi were screened for growth and reduction of soluble organic compounds, carbohydrates, and protein from stillage to identify species capable of rapidly concentrating organic compounds into readily separable biomass in an attempt to concentrate the product using a much more efficient centrifugation step. Yeasts amenable to production of biomass derived products including bio-oils (Yarrowia lipolytica and Rhodotorula pallida), chitosan (Aspergillus niger) and animal feed (Cyberlindnera jadinii) were identified as well as microbes capable of efficient production of small organic acids with applications as bioderived polymers including 3-hydroxypropionic acid (engineered A. niger) and lactic acid using a co-culture of Debaryomyces udenii and Lactobacillus pentosus. The filamentous fungus A. niger eliminated all specifically measured soluble organics (glycerol, acetate, lactate, ethanol, and citrate) in under 48 hours and reduced total soluble protein content by 46% and total carbohydrate content by 83% within 96 hours, the greatest reduction in organic content observed. During this process an A. niger strain engineered to produce 3-hydroxypropionic acid achieved a yield of 0.35 C-mol 3HP / C-mol non-protein organics consumed at an overall rate of 0.09 g/Lh in unmodified stillage without pH control. Stillage treated by the fodder yeast C. jadinii as well as stillage containing acetic or lactic acid was found to be most suitable for growth by electrogenic bacteria with applications in production of electricity or hydrogen from wastewater. This work establishes fungal and bacterial strains appropriate for biological treatment of stillage to produce biomass derived products, soluble commodity chemicals, energy, and treated water to reduce the energy intensity and improve the economics of ethanol biorefineries.

09 BIOMASS FUELS↗
DOE OSTI2024

Modeling prebiotic chemistries with quantum accuracy at classical costs

Molecular Dynamics (MD) simulations using classical force-fields are commonly employed in numerous scientific investigations. However, many natural processes involve bond breaking and quantum forces. This complexity is compounded by the presence of multiple competing length and timescales. For example, accurately modeling the thermodynamics and dynamics of a chemical reaction requires accounting for the concerted movements of numerous solvent molecules and ions with their own fast or slow timescales. While widely used static Density Functional Theory (DFT) calculations at 0 temperature can be beneficial for such investigations, they do not account for dynamics, and lack precision in describing the molecular environments. They particularly fail at correct, rigorous treatments of finite-temperature fluctuations, and thus generalization to experimentally relevant conditions. In PNAS Benayad et al develop a scalable, generalizable approach for designing Neural Network Potentials (NNPs) that can handle chemical reactivity in solvated systems with quantum accuracy at classical costs. Specifically, they study phosphoester bond formation and rupture, which is fundamentally relevant to the Phosphorus-Oxygen bond formation central to life, and especially for the RNA world hypothesis. The framework developed here has the potential to generalize to different chemical reactions of energy and biological relevance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method, we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology is benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We apply this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detect 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of phosphorylation events relevant to mitochondrial and brain biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗