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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Coupled Microbial-Conversion and Computational-Fluid-Dynamics (CFD) Models for Butanediol Production in Micro-Aerated Reactors

Microbial conversion of substrates to macromolecules has been widely used in the synthesis of value-added products in pharmaceutical and biotechnology industries. These bioreactions are also being investigated in the production of low-value commodities such as biofuels [1]. Gas-liquid mass-transfer and transport-reaction coupling are important challenges when designing and scaling up these reactor systems. Experiments in wellmixed small-scale reactors have enabled characterization of microbial reactivity, while their coupling with macroscale transport remains relatively unexplored. In this work, we use a coupled metabolic-CFD model to study the action of a genetically engineered microbe Zymomonas mobilis [2] on sugars to produce 2,3-Butanediol (BDO). BDO is an important hydrocarbon intermediate that can be catalytically upgraded to several fuels and chemicals [3]. An important aspect to this particular microbial conversion is the need for micro-aerated environments as opposed to traditional aerobic fermentation. Slight variations in oxygen concentration can result in competing reaction pathways that disable BDO production. Hence, gas-liquid mass transfer and transport need to be optimized in large-scale reactors to maximize BDO production, for which CFD is a valuable tool. The aerobic-fermentation CFD model previously developed by the authors [5] for simulating bubble-column and airlift reactors at scale was used in this study. The Reynolds-averaged mass, momentum and energy transport equations for interpenetrating gas and liquid phase are solved in this model along with the transport and interphase mass transfer of oxygen. Our previous work used a phenomenological model for microbial oxygen uptake that neglected microbial growth and other reaction pathways. In this work, a detailed metabolic model enabled prediction of product formation and inhibition pathways. In order to manage computational cost, we used a subcycling technique [6] that takes advantage of the clear separation in transport (~ 200 sec) and reaction (~ 2-3 hours) timescales. The CFD model is first solved to steady state, after which the metabolic model is advanced at every cell in the computational domain using the local oxygen concentration. The CFD model is then run to achieve a new steady state that provides a new oxygen distribution for the metabolic model. This process, where reaction and fluid updates are interleaved together, is iterated until reactants are completely exhausted. This work will examine the performance of different reactor designs such as bubble column and airlift reactors at scale (250-500 m3). Oxygen mass-transfer coefficient and distribution are critically analyzed among reactors, and optimization studies pertaining to aeration is presented. Furthermore, it has been observed in experiments that high BDO production may be achieved by manipulating the aerobic environment over the course of reaction, such that oxygen concentration is high during the growth phase, and very low as sugar is depleted. This characteristic will be addressed by our simulations for which a timedependent scheduling strategy for aeration is presented that maximizes BDO production. [1] Humbird, D., Davis, R., and McMillan, J., Aeration costs in stirred-tank and bubble column bioreactors, Biochemical Engineering Journal, 127, 161—166, 2017 [2] Yang, S., Mohagheghi, A., Franden, M. A., Chou, Y.-C., Chen, X., Dowe, N., Himmel, M. E., and Zhang, M., Metabolic engineering of zymomonas mobilis for 2, 3-butanediol production from lignocellulosic biomass sugars. Biotechnology for biofuels, 9(1):189, 2016 [3] Kim, S. J., Sim, H. J., Kim, J. W., Lee, Y. G., Park, Y. C., and Seo, J. H., Enhanced production of 2,3-butanediol from xylose by combinatorial engineering of xylose metabolic pathway and cofactor regeneration in pyruvate decarboxylase-deficient Saccharomyces cerevisiae. Bioresource Technology, 245:1551–1557, 2017 [4] Weller, H., Tabor, G., Jasak, H. and Fureby, C., A tensorial approach to computational continuum mechanics using object-oriented techniques, Computers in physics, 12, 6, 620--631, 1998

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
NASA NTRS1986

Amphibian egg cytoplasm response to altered g-forces and gravity orientation

Elucidation of dorsal/ventral polarity and primary embryonic axis development in amphibian embryos requires an understanding of cytoplasmic rearrangements in fertile eggs at the biophysical, physiological, and biochemical levels. Evidence is presented that amphibian egg cytoplasmic components are compartmentalized. The effects of altered orientation to the gravitational vector (i.e., egg inversion) and alterations in gravity force ranging from hypergravity (centrifugation) to simulated microgravity (i.e., horizontal clinostat rotation) on cytoplasmic compartment rearrangements are reviewed. The behavior of yolk compartments as well as a newly defined (with monoclonal antibody) nonyolk cytoplasmic compartment, in inverted eggs and in eggs rotated on horizontal clinostats at their buoyant density, is discussed.

Neff, A. W.↗
DOE OSTI2025

Enzymatic carbon–fluorine bond cleavage by human gut microbes

Fluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated compounds enter the human body through food, water, and xenobiotics including pharmaceuticals, exposing gut microbes to these substances. The human gut microbiota is known for its xenobiotic biotransformation capabilities, but it was not previously known whether gut microbial enzymes could break carbon-fluorine bonds, potentially altering the toxicity of these compounds. Here, through the development of a rapid, miniaturized fluoride detection assay for whole-cell screening, we identified active gut microbial defluorinases. We biochemically characterized enzymes from diverse human gut microbial classes including Clostridia, Bacilli, and Coriobacteriia, with the capacity to hydrolyze (di)fluorinated organic acids and a fluorinated amino acid. Whole-protein alanine scanning, molecular dynamics simulations, and chimeric protein design enabled the identification of a disordered C-terminal protein segment involved in defluorination activity. Domain swapping exclusively of the C-terminus conferred defluorination activity to a nondefluorinating dehalogenase. To advance our understanding of the structural and sequence differences between defluorinating and nondefluorinating dehalogenases, we trained machine learning models which identified protein termini as important features. Models trained on 41-amino acid segments from protein C termini alone predicted defluorination activity with 83% accuracy (compared to 95% accuracy based on full-length protein features). This work is relevant for therapeutic interventions and environmental and human health by uncovering specificity-determining signatures of fluorine biochemistry from the gut microbiome.

Probst, Silke I↗
DOE OSTI2020

The hTERT core promoter forms three parallel G-quadruplexes

The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Ultrastructural and cellular mechanisms in myocardial deconditioning in weightlessness

The cardiovascular deconditioning that has been shown to result from immobilization on earth and in the microgravity environment during spaceflight is considered. The major interests to future long-term spaceflight are the determination of the specific factors causing myocardial deconditioning, the irreversibility/reversibility of the changes, and preventative/treatment methods for this deconditioning process. The results of earlier animal studies designed to determine the effects of immobilization on myocardial function demonstrate that both ultrastructural and functional changes occur during test periods ranging from 14 days to 6 months. Based on such results and the need for a more precise understanding of the structural and biochemical mechanisms leading to these effects, an experiment was designed for use in future studies. The results of the Cosmos 1887 and 2044 flights as well as their comparison and analysis indicate that significant differences exist between simulated and actual spaceflight subjects. Spaceflight subjects demonstrate greater changes than tail-suspended subjects. More spaceflight studies will be necessary to gain a greater understanding of the basic mechanism behind myocardial deconditioning resulting from spaceflight and the most effective methods to be utilized in its prevention and treatment.

Philpott, Delbert E.↗
DOE OSTI2022

Allosteric inhibition of HTRA1 activity by a conformational lock mechanism to treat age-related macular degeneration

The trimeric serine protease HTRA1 is a genetic risk factor associated with geographic atrophy (GA), a currently untreatable form of age-related macular degeneration. Here, we describe the allosteric inhibition mechanism of HTRA1 by a clinical Fab fragment, currently being evaluated for GA treatment. Using cryo-EM, X-ray crystallography and biochemical assays we identify the exposed LoopA of HTRA1 as the sole Fab epitope, which is approximately 30 Å away from the active site. The cryo-EM structure of the HTRA1:Fab complex in combination with molecular dynamics simulations revealed that Fab binding to LoopA locks HTRA1 in a non-competent conformational state, incapable of supporting catalysis. Moreover, grafting the HTRA1-LoopA epitope onto HTRA2 and HTRA3 transferred the allosteric inhibition mechanism. This suggests a conserved conformational lock mechanism across the HTRA family and a critical role of LoopA for catalysis, which was supported by the reduced activity of HTRA1-3 upon LoopA deletion or perturbation. This study reveals the long-range inhibition mechanism of the clinical Fab and identifies an essential function of the exposed LoopA for activity of HTRA family proteases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗
DOE OSTI2021

Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

Significance Breakthrough technological advances such as Hi-C have enabled large-scale sequencing of pairwise genomic contacts. However, translating the 2D contacts to 3D spatial models remains challenging. Here we develop the “4DHiC” modeling method to infer 3D information from 2D datasets across time and construct a 3D model of the inactive X-chromosome (Xi). Our model not only demonstrates a spatial phase-separation between A/B and S1/S2 compartments to form “hemispheres,” but also reveals persistent smaller-scale structures hidden under the Xi superstructure. We also simulate Xist RNA spreading dynamics and deduce that the RNA spreads between hemispheres via both surface and core to establish the Xi. Our 4DHiC will serve a growing demand for data-driven methodologies that extract spatial information from biochemical interaction data.

Lappala, Anna↗
NASA NTRS1984

Effects of suspension on tissue levels of glucocorticoid receptors

Differential muscle responses can be simulated by hypokinetic/hypodynamic (H/H) suspension of rats with complete unloading of the hindlimb muscles. Since mechanism(s) underlying these atrophic effects were not clearly elucidated, experiments were initiated to investigate a possible role for glucocorticoids in the physiological and biochemical responses to H/H. The principal objective was to assess the potential for alterations in peripheral responsiveness to glucocorticoids in response to H/H. Studies have initially focused on the determination of tissue levels of glucocorticoid receptors as one index of hormonal sensitivity at the cellular level. Four hindlimb muscles (soleus, gastrocnemius, plantaris and EDL), previously demonstrated to exhibit differential responses to H/H, were investigated. Receptor levels in other glucocorticoid sensitive tissues (heart, liver, and kidney) were determined. Male rats (180-200g) were suspended for 7 or 14 days, sacrificed by cervical dislocation, and the tissues excised.

Steffen, J. M.↗
NASA NTRS1990

Spaceflight effects on biomechanical and biochemical properties of rat vertebrae

The biomechanical and biochemical responses of lumbar vertebral bodies during a 12.5-day spaceflight (Cosmos 1887 biosatellite) were determined for rapidly growing rats (90-day-old, Czechoslovakian-Wistar). By use of age-matched vivarium controls (normal cage environment) and synchronous controls (simulated flight conditions), as well as a basal control group (killed before lift-off on the 1st day of flight), the combined influences of growth and space-flight could be examined. Centra of the sixth lumbar vertebrae (L6) were compressed to 50% strain at a fast strain rate while immersed in physiological buffer (37 degrees C). The body masses of vivarium and synchronous controls were significantly heavier than either the flight or basal controls. The flight group had an L6 vertebral body compressional stiffness that was 39% less than the vivarium controls, 47% less than the synchronous control, and 16% less than the basal controls. In addition, the average initial maximum load of the flight L6 was 22% less than vivarium controls and 18% less than the synchronous controls, whereas the linear compressional load of the flight group averaged 34% less than the vivarium and 25% less than the synchronous groups. The structural properties of the vertebrae from the 12.5-day-younger basal group closely resembled the flight vertebrae. Calcium, phosphorous, and hydroxyproline concentrations were not significantly different among the groups. Nevertheless, the lack of strength and stiffness development in spaceflight, coupled with a smaller proportion of mature hydroxypyridinoline cross-links, suggested that the 12.5 days of spaceflight slowed the maturation of trabecular bone in the vertebral bodies of rapidly growing rats.

Non-NASA Center↗
DOE OSTI2021

Rational Enzyme Design for Controlled Functionalization of Acetylated Xylan for Cell-Free Polymer Biosynthesis

Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.

93 SC - Biological and Environmental Research (BER↗
NASA NTRS1992

Metabolic energy requirements for space flight

The international space community, including the USSR, Japan, Germany, the European Space Agency, and the US, is preparing for extended stays in space. Much of the research planned for space will be tended by humans, thus, maintaining adequate nutritional status during long stays in space has lately become an issue of much interest. Historically, it appears that minimum nutritional requirements are being met during stays in space. Thus far, crewmembers have been able to consume food adequate for maintaining nominal performance in microgravity. The physiological data obtained from ground-based and flight research that may enable us to understand the biochemical alterations that effect energy utilization and performance. Focus is on energy utilization during the Apollo lunar missions, Skylab's extended space lab missions, and Space Shuttle flights. Available data includes those recorded during intra- and extravehicular activities as well as during microgravity simulation (bed rest). Data on metabolism during flight and during bed rest are discussed, with a follow-up on human gastrointestinal function.

Lane, Helen W.↗
NASA NTRS2017

Responses of Cardiac Tissue to Simulated Weightlessness

Our current study aims to determine the molecular mechanisms that underlie these cardiac changes in response to spaceflight. The central hypothesis of our study is that long duration simulated weightlessness and subsequent recovery causes select and persistent changes in gene expression and oxidative defense-related pathways. In this study, we will first conduct general analyses of three-month old male and female animals, focusing on two key long-duration time points, (i.e. after 90 days of simulated weightlessness (HU) and after 90 days recovery from 90 days of HU. Both rat-specific gene arrays and qPCR will be performed focusing on genes already implicated in oxidative stress responses and cardiac disease. Gene expression analyses will be complemented by biochemical tests of frozen tissue lysates for select markers of oxidative damage.

heart↗
NASA NTRS1992

Inactivation of a model coliphage virus in water by iodine

Until now, NASA's space water reuse research program has not considered the transport of water-borne infectious enteric viruses; however, viral diseases probably are a signifficant concern in long-duration space missions. To simplify monitoring and prediction of pathogen distribution, model indicator strains historically have been used. In this research, the male specific RNA coliphage MS-2 is used as a model of enteric viruses due to their similar size and biochemical composition. Inactivation of some water-borne enteric viruses by iodine has previously been characterized. In this paper, iodine inactivation of the model coliphage MS-2 in buffered water is compared with earlier bench-scale disinfection survival data and with survival in iodinated simulated shower water used in a test water recycling system.

Brion, Gail M.↗
DOE OSTI2022

Effect of biomass liquefaction on glucose and xylose prices predicted by National Renewable Energy Laboratory biochemical sugar model

Abstract The National Renewable Energy Laboratory (NREL) published a model in 2017 that enables the minimum selling price of lignocellulosic sugar to be calculated. The model can be modified to suit any biomass feedstock and operational design. In the present case, the model is used to understand the economics of a process configuration that incorporates liquefaction as a preprocessing step in corn‐stover‐fed biorefinery. This study demonstrates a quantitative approach utilizing an existing biorefinery setup to simulate the biomass liquefaction technique while estimating the price of the resulting sugar product. The objective is to understand whether the addition of liquefaction methodology – and the substitution of acid pretreatment – can reduce the cost of lignocellulosic sugars. The reason for setting up a liquefaction unit at the start is to reduce the yield stress of biomass slurry so that the flow remains unrestricted downstream. The liquefaction process is also unique because it uses no chemicals and saves the cost of pretreatment. The pretreatment step is bypassed because the output of liquefaction can be fed into enzyme hydrolysis just after simple cooking. The liquefaction process can be performed in three modes: enzyme, enzyme mimetic, and a combination of enzyme and enzyme mimetic. The results from the BC1707 model indicate the minimum cost for the enzyme liquefaction route. © 2022 The Authors. Biofuels, Bioproducts and Biorefining published by Society of Industrial Chemistry and John Wiley & Sons Ltd.

09 BIOMASS FUELS↗
NASA NTRS2002

Laboratory Studies of Extraterrestrial Ices and PAHs: Making an Astrobiological Silk Purse Out of An Interstellar Sow's Ear

Tremendous strides have been made in our understanding of interstellar material over the past twenty years thanks to significant, parallel developments in observational astronomy and laboratory astrophysics. Today, the composition of dust in the ISM is reasonably well constrained to cold, micron-sized particles of various refractory materials. Shrouded within the protective confines of cold, opaque molecular clouds--the birthplace of stars and planets--these particles secrete mantles of mixed molecular lees whose major components are also well constrained. Finally, amidst the molecular inventory of these ice mantles are likely to be found polycyclic aromatic hydrocarbons (PAHs), whose telltale infrared signature I is now recognized throughout the Universe. However, of what significance is this scenario to the origin of life in our solar system--or any other? The major components of the icy materials observed in interstellar clouds and in our own solar system are uniformly quite simple. In addition, despite the fact that PAHs likely represent the single largest molecular reservoir of organic carbon in evolving planetary systems, they are not what would be considered "biogenic" molecules. Although interesting from a chemical and astrophysical standpoint, in the absence of a mechanism by which these materials can be transformed into more biochemically significant structures, they are of little Astrobiological significance. In this talk, we will begin with a brief review of the nature and abundance of the "raw" population of PAHs and PAH-related materials in the ISM. From there, we will move on to explore our laboratory simulations of the photochemical evolution of realistic mixed molecular ices under conditions which simulate those encountered in the ISM and in evolving planetary systems. Particular attention will be paid to the surprisingly complex array of organic species that are produced in these ices from such a deceptively simple inventory of starting materials. In addition, we will explore the chemistry of PAHs under these conditions and consider its potential for transforming that rich repository of pre-biotic organic "ore" into materials of greater importance to Astrobiology.

Hudgins, Douglas M.↗
DOE OSTI2026

Process Optimization and Real-Time Control of Synergistic Microalgae Cultivation and Wastewater Treatment (Final Technical Report)

The overarching goal of this work was to accelerate the commercialization of high productivity, mixed community microalgal treatment technologies for the synergistic treatment of wastewater and the production of biofuel feedstocks. This project addressed a critical barrier to the financial viability and energy efficiency of algal wastewater treatment: an inability to design and operate high-rate processes that reliably achieve target effluent qualities, areal productivities, and biochemical compositions (lipid, protein, carbohydrate content) despite fluctuations in wastewater composition, weather, and microbial communities. Key outcomes from this work include an optimized and controlled Advanced Biological Nutrient Recovery (ABNR) design as well as a suite of open-source tools that include a calibrated and validated algae process simulator in QSDsan and a novel low-cost, real-time microbial monitoring tool. These tools can be leveraged by other algal cultivation and wastewater treatment technology developers in future work.

09 BIOMASS FUELS↗