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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 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Two Pathways for Glutamate Biosynthesis in the Syntrophic Bacterium Syntrophus aciditrophicus

Here, the anaerobic metabolism of crotonate, benzoate, and cyclohexane carboxylate by Syntrophus aciditrophicus grown syntrophically with Methanospirillum hungatei provides a model to study syntrophic cooperation. Recent studies revealed that S. aciditrophicus contains Re -citrate synthase but lacks the common Si-citrate synthase. To establish whether the Re-citrate synthase is involved in glutamate synthesis via the oxidative branch of the Krebs cycle, we have used [1- 13 C]acetate and [1- 14 C]acetate as well as [ 13 C]bicarbonate as additional carbon sources during axenic growth of S. aciditrophicus on crotonate. Our analyses showed that labeled carbons were detected in at least 14 amino acids, indicating the global utilization of acetate and bicarbonate. The labeling patterns of alanine and aspartate verified that pyruvate and oxaloacetate were synthesized by consecutive carboxylations of acetyl coenzyme A (acetyl-CoA). The isotopomer profile and 13 C nuclear magnetic resonance (NMR) spectroscopy of the obtained [ 13 C]glutamate, as well as decarboxylation of [ 14 C]glutamate, revealed that this amino acid was synthesized by two pathways. Unexpectedly, only the minor route used Re -citrate synthase (30 to 40%), whereas the majority of glutamate was synthesized via the reductive carboxylation of succinate. This symmetrical intermediate could have been formed from two acetates via hydration of crotonyl-CoA to 4-hydroxybutyryl-CoA. 4-Hydroxybutyrate was detected in the medium of S. aciditrophicus when grown on crotonate, but an active hydratase could not be measured in cell extracts, and the annotated 4-hydroxybutyryl-CoA dehydratase (SYN_02445) lacks key amino acids needed to catalyze the hydration of crotonyl-CoA. Besides Clostridium kluyveri , this study reveals the second example of a microbial species to employ two pathways for glutamate synthesis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes

Recently, methanogenic archaea belonging to the genus Methanothrix were reported to have a fundamental role in maintaining stable ecosystem functioning in anaerobic bioreactors under different configurations/conditions. In this study, we reconstructed three Methanothrix metagenome-assembled genomes (MAGs) from granular sludge collected from saline upflow anaerobic sludge blanket (UASB) reactors, where Methanothrix harundinacea was previously implicated with the formation of compact and stable granules under elevated salinity levels (up to 20 g/L Na + ). Genome annotation and pathway analysis of the Methanothrix MAGs revealed a genetic repertoire supporting their growth under high salinity. Specifically, the most dominant Methanothrix (MAG_279), classified as a subspecies of Methanothrix_A harundinacea_D, had the potential to augment its salinity resistance through the production of different glycoconjugates via the N-glycosylation process, and via the production of compatible solutes as N ε -acetyl-β-lysine and ectoine. The stabilization and reinforcement of the cell membrane via the production of isoprenoids was identified as an additional stress-related pathway in this microorganism. The improved understanding of the salinity stress-related mechanisms of M. harundinacea highlights its ecological niche in extreme conditions, opening new perspectives for high-efficiency methanisation of organic waste at high salinities, as well as the possible persistence of this methanogen in highly-saline natural anaerobic environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evolving a New Electron Transfer Pathway for Nitrogen Fixation Uncovers an Electron Bifurcating-Like Enzyme Involved in Anaerobic Aromatic Compound Degradation

There is increasing evidence that protein electron carriers like Fd evolved to form specific partnerships with select electron donors and acceptors to keep native electron transfer pathways insulated from one another. This makes it challenging to integrate a Fd-dependent pathway such as biological nitrogen fixation into non-nitrogen-fixing organisms and provide the high-energy reducing power needed to fix nitrogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean

Microbes play a significant role in the degradation of petroleum hydrocarbons in the oceans, yet little is known about the native bacteria that metabolize hydrocarbons before an oil spill. The Faroe-Shetland Channel (FSC) is a deepwater subarctic region of the North Atlantic with prominent oil production and a diverse microbial community associated with the degradation of petroleum. Here, we combine DNA-based stable-isotope probing (DNA-SIP) with metagenomics to elucidate the metabolic underpinnings of native alkane-degrading bacteria from the FSC. From two 13C n-hexadecane SIP experiments using seawater from 5 and 700 m depths in the FSC, we obtained 42 metagenome-assembled genomes (MAGs) belonging to 19 genera, including two previously overlooked hydrocarbon-degrading bacteria, Lentibacter (Alphaproteobacteria) and Dokdonia (Bacteroidetes). Diversity surveys indicated Lentibacter were dominant members of the FSC, constituting up to 17% of these communities. Many of the SIP-enriched MAGs (20/42) encoded a complete alkane oxidation pathway, including alkane monooxygenase (AlkB), rubredoxin reductase (AlkT), and rubredoxin-2 (AlkG). Fourteen Aphaproteobacteria MAGs lacked AlkG for electron transfer. Instead, they encoded novel disulfide isomerases with iron-binding cysteine motifs conserved across rubredoxins. Dokdonia lacked AlkT and AlkG, however, their central alkane-degradation catabolic pathways were complete. We describe previously unrecognized bacteria capable of hydrocarbon degradation, including the dominant genera Lentibacter, which may continuously purge hydrocarbons released from oil exploration activities in the FSC. This advances the understanding of the diversity and physiologies of alkane degradation in the North Atlantic and provides evidence of new mechanisms used to metabolize alkanes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

Background: Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. Results: We demonstrate that chronic exposure to ecologically relevant concentrations of glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, induce significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the “Reactome,” we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways, and collagen degradation, responsible for the repair of wounds and tissue remodeling. Conclusions: Our results show that chronic exposure to concentrations of Roundup and glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways

Stimulus-induced perturbations from the steady state are a hallmark of signal transduction. In some signaling modules, the steady state is characterized by rapid synthesis and degradation of signaling proteins. Conspicuous among these are the p53 tumor suppressor, its negative regulator Mdm2, and the negative feedback regulator of NFkB, IkBa. We investigated the physiological importance of this turnover, or flux, using a computational method that allows flux to be systematically altered independently of the steady state protein abundances. Applying our method to a prototypical signaling module, we show that flux can precisely control the dynamic response to perturbation. Next, we applied our method to experimentally validated models of p53 and NFkB signaling. We find that high p53 flux is required for oscillations in response to a saturating dose of ionizing radiation (IR). In contrast, high flux of Mdm2 is not required for oscillations but preserves p53 sensitivity to sub-saturating doses of IR. In the NFkB system, degradation of NFkB-bound IkB by the IkB kinase (IKK) is required for activation in response to TNF, while high IKK-independent degradation prevents spurious activation in response to metabolic stress or low doses of TNF. Our work identifies flux pairs with opposing functional effects as a signaling motif that controls the stimulus-sensitivity of the p53 and NFkB stress-response pathways, and may constitute a general design principle in signaling pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response

Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae , the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. We developed an approach to link predicted regulators to groups of likely co-regulated phospho-peptides responding to stress, thereby creating new edges in a background protein interaction network. We then use integer linear programming (ILP) to integrate wild type and mutant phospho-proteomic data and predict the network controlling stress-activated phospho-proteomic changes. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Conclusively, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways

During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g., H 2 ), and by reverse electron flow from the photosynthetic electron transport chain. These electrons are stored as reduced electron-carrying cofactors (e.g., NAD(P)H and ferredoxin). The overall ratio of oxidized to reduced cofactors (e.g., NAD(P)+:NAD(P)H), or ’redox poise’, is difficult to understand or predict, as are the cellular processes for dissipating these reducing equivalents. Using physics-based models that capture mass action kinetics consistent with the thermodynamics of reactions and pathways, a range of redox conditions for heterophototrophic growth are evaluated, from conditions in which the NADP+/NADPH levels approach thermodynamic equilibrium to conditions in which the NADP+/NADPH ratio is far above the typical physiological values. Modeling predictions together with experimental measurements indicate that the redox poise of the cell results in large-scale changes in the activity of biosynthetic pathways and, thus, changes in cell macromolecule levels (DNA, RNA, proteins, and fatty acids). Furthermore, modeling predictions indicate that during phototrophic growth, reverse electron flow from the quinone pool is a minor contributor to the production of reduced cofactors (e.g., NAD(P)H) compared to other oxidative processes (H 2 and carbon substrate oxidation). Instead, the quinone pool primarily operates to aid ATP production. The high level of ATP, in turn, drives reduction processes even when NADPH levels are relatively low compared to NADP+ by coupling ATP hydrolysis to the reductive processes. The model, in agreement with experimental measurements of macromolecule ratios of cells growing on different carbon substrates, indicates that the dynamics of nucleotide versus lipid and protein production is likely a significant mechanism of balancing oxidation and reduction in the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8

Antibody 10E8 targets the membrane-proximal external region (MPER) of HIV-1 gp41, neutralizes >97% of HIV-1 isolates, and lacks the auto-reactivity often associated with MPER-directed antibodies. The developmental pathway of 10E8 might therefore serve as a promising template for vaccine design, but samples from time-of-infection—often used to infer the B cell record—are unavailable. In this study, we used crystallography, next-generation sequencing (NGS), and functional assessments to infer the 10E8 developmental pathway from a single time point. Mutational analysis indicated somatic hypermutation of the 2nd-heavy chain-complementarity determining region (CDR H2) to be critical for neutralization, and structures of 10E8 variants with V-gene regions reverted to genomic origin for heavy-and-light chains or heavy chain-only showed structural differences >2 Å relative to mature 10E8 in the CDR H2 and H3. To understand these developmental changes, we used bioinformatic sieving, maximum likelihood, and parsimony analyses of immunoglobulin transcripts to identify 10E8-lineage members, to infer the 10E8-unmutated common ancestor (UCA), and to calculate 10E8-developmental intermediates. We were assisted in this analysis by the preservation of a critical D-gene segment, which was unmutated in most 10E8-lineage sequences. UCA and early intermediates weakly bound a 26-residue-MPER peptide, whereas HIV-1 neutralization and epitope recognition in liposomes were only observed with late intermediates. Antibody 10E8 thus develops from a UCA with weak MPER affinity and substantial differences in CDR H2 and H3 from the mature 10E8; only after extensive somatic hypermutation do 10E8-lineage members gain recognition in the context of membrane and HIV-1 neutralization.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Exploring innovative pathway for SRF cavity fabrication

This article shows a study on an alternative pathway for the fabrication of a complete 1.3 GHz SRF cavity, aiming at improving production reliability, reducing the use of chemical polishing (EP or BCP) which is a costly and safety-critical step, and preserving surface quality after forming. Unlike the conventional pathway, the fabrication process is performed after polishing. This point is crucial as the used polishing technology could be applied only to flat geometries. The performed investigation demonstrates that damages during the fabrication process are considered minor, localized, and limited to the near-surface. Moreover, these studies confirm that the damaged layer (100-200 µm) is mainly caused by the rolling process, and not by the subsequent fabrication steps. A laser confocal microscope and SEM-EBSD technique were used to compare samples before and after forming. The preliminary results are discussed and presented in this paper.

Hryhorenko, O.↗
DOE OSTI2013

Whole Algae Hydrothermal Liquefaction Technology Pathway

In support of the Bioenergy Technologies Office, the National Renewable Energy Laboratory (NREL) and the Pacific Northwest National Laboratory (PNNL) are undertaking studies of biomass conversion technologies to hydrocarbon fuels to identify barriers and target research toward reducing conversion costs. Process designs and preliminary economic estimates for each of these pathway cases were developed using rigorous modeling tools (Aspen Plus and Chemcad). These analyses incorporated the best information available at the time of development, including data from recent pilot and bench-scale demonstrations, collaborative industrial and academic partners, and published literature and patents. This pathway case investigates the feasibility of using whole wet microalgae as a feedstock for conversion via hydrothermal liquefaction. Technical barriers and key research needs have been assessed in order for the hydrothermal liquefaction of microalgae to be competitive with petroleum-derived gasoline, diesel and jet range blendstocks.

algae↗
DOE OSTI2013

Algal Lipid Extraction and Upgrading to Hydrocarbons Technology Pathway

This technology pathway case investigates the cultivation of algal biomass followed by further lipid extraction and upgrading to hydrocarbon biofuels. Technical barriers and key research needs have been assessed in order for the algal lipid extraction and upgrading pathway to be competitive with petroleum-derived gasoline-, diesel-, and jet-range hydrocarbon blendstocks.

09 BIOMASS FUELS↗
DOE OSTI2013

Catalytic Upgrading of Sugars to Hydrocarbons Technology Pathway

This technology pathway case investigates the catalytic conversion of solubilized carbohydrate streams to hydrocarbon biofuels, utilizing data from recent efforts within the National Advanced Biofuels Consortium (NABC) in collaboration with Virent, Inc. Technical barriers and key research needs that should be pursued for the catalytic conversion of sugars pathway to be competitive with petroleum-derived gasoline-, diesel-, and jet-range hydrocarbon blendstocks have been identified.

09 BIOMASS FUELS↗
DOE OSTI2013

Ex-Situ Catalytic Fast Pyrolysis Technology Pathway

This technology pathway case investigates converting woody biomass using ex-situ catalytic fast pyrolysis followed by upgrading to gasoline-, diesel-, and jet-range hydrocarbon blendstocks. Technical barriers and key research needs that should be pursued for this pathway to be competitive with petroleum-derived blendstocks have been identified.

09 BIOMASS FUELS↗
DOE OSTI2013

Biological Conversion of Sugars to Hydrocarbons Technology Pathway

This technology pathway case investigates the biological conversion of biomass-derived sugars to hydrocarbon biofuels, utilizing data from recent literature references and information consistent with recent pilot-scale demonstrations at NREL. Technical barriers and key research needs have been identified that should be pursued for the pathway to become competitive with petroleum-derived gasoline-, diesel-, and jet-range hydrocarbon blendstocks.

09 BIOMASS FUELS↗
DOE OSTI2013

In-Situ Catalytic Fast Pyrolysis Technology Pathway

This technology pathway case investigates converting woody biomass using in-situ catalytic fast pyrolysis followed by upgrading to gasoline-, diesel-, and jet-range hydrocarbon blendstocks. Technical barriers and key research needs that should be pursued for this pathway to be competitive with petroleum-derived blendstocks have been identified.

09 BIOMASS FUELS↗
DOE OSTI2013

Low-e Storm Windows: Market Assessment and Pathways to Market Transformation

Laboratory and field studies sponsored by the U.S. Department of Energy (DOE) demonstrate that the use of low-emissivity (low-e) storm windows can lead to significant heating and cooling energy savings in homes. This report examines the market for low-e storm windows based on market data, case studies, and recent experience with weatherization deployment programs. It uses information from interviews conducted with DOE researchers and industry partners involved in case studies and early deployment efforts related to low-e storm windows. In addition, this study examines potential barriers to market acceptance, assesses the market and energy savings potential, and identifies opportunities to transform the market for low-e storm windows and overcome market adoption barriers. Based on laboratory testing, case studies, and climate-based modeled energy savings, the installation of low-e storm windows is estimated to reduce heating and cooling consumption by 12 to 33% in residential homes. Individual home savings would depend on the overall condition of existing windows and home as well as climate conditions. Based on these heating and cooling saving ranges, low-e storm windows have a technical potential energy savings – that is, the energy savings that would result if all low-performing windows were covered with low-e storm windows – ranging from 0.7 to 1.96 quadrillion Btus primary (source) energy. Of this technical potential, this study estimates that market adoption of low-e storm windows could reasonably achieve savings of 140 trillion Btus of primary energy annually by 2025, assuming DOE implements a number of market transformation activities directed toward low-e storm window market adoption. To assess the marketability and market adoption potential of low-e storm windows, this study examines and characterizes the benefits and costs of the technology, the size and characteristics of likely target markets, the potential pathways to reach these markets, possible market barriers, and the likelihood of overcoming these barriers. A number of promising market transformation pathways are identified including existing weatherization assistance programs, utility energy-efficiency incentive programs, federally sponsored energy efficiency retrofit programs, standards and rating organizations, and federal building energy-efficiency mandates and programs. By working with storm window manufacturers, installers, energy-efficiency consortiums, and the Federal Energy Management Program, the U.S. Department of Energy’s Building America program could implement a number of targeted outreach, education, and technical assistance programs to help effectively transform the market for low-e storm windows and have a measurable impact on reducing residential energy consumption over time.

Building America↗
DOE OSTI2014

All-Pathways Dose Analysis for the Portsmouth On-Site Waste Disposal Facility (OSWDF)

A Portsmouth On-Site Waste Disposal Facility (OSWDF) All-Pathways analysis has been conducted that considers the radiological impacts to a resident farmer. It is assumed that the resident farmer utilizes a farm pond contaminated by the OSWDF to irrigate a garden and pasture and water livestock from which food for the resident farmer is obtained, and that the farmer utilizes groundwater from the Berea sandstone aquifer for domestic purposes (i.e. drinking water and showering). As described by FBP 2014b the Hydrologic Evaluation of Landfill Performance (HELP) model (Schroeder et al. 1994) and the Surface Transport Over Multiple Phases (STOMP) model (White and Oostrom 2000, 2006) were used to model the flow and transport from the OSWDF to the Points of Assessment (POAs) associated with the 680-ft elevation sandstone layer (680 SSL) and the Berea sandstone aquifer. From this modeling the activity concentrations radionuclides were projected over time at the POAs. The activity concentrations were utilized as input to a GoldSimTM (GTG 2010) dose model, described herein, in order to project the dose to a resident farmer over time. A base case and five sensitivity cases were analyzed. The sensitivity cases included an evaluation of the impacts of using a conservative inventory, an uncased well to the Berea sandstone aquifer, a low waste zone uranium distribution coefficient (Kd), different transfer factors, and reference person exposure parameters (i.e. at 95 percentile). The maximum base case dose within the 1,000 year assessment period was projected to be 1.5E-14 mrem/yr, and the maximum base case dose at any time less than 10,000 years was projected to be 0.002 mrem/yr. The maximum projected dose of any sensitivity case was approximately 2.6 mrem/yr associated with the use of an uncased well to the Berea sandstone aquifer. This sensitivity case is considered very unlikely because it assumes leakage from the location of greatest concentration in the 680 SSL in to the Berea sandstone aquiver over time and does not conform to standard private water well construction practices. The bottom-line is that all predicted doses from the base case and five sensitivity cases fall well below the DOE all-pathways 25 mrem/yr Performance Objective.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗