SEARCH · Engineering Papers
Results for “pathways”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
In situ TEM imaging of CaCO3 nucleation reveals coexistence of direct and indirect pathways
Explore the source record for details and available documents.
Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway
Abstract not provided
The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea
Not provided.
Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria
ABSTRACT Brucella abortus σ E1 is an EcfG family sigma factor that regulates the transcription of dozens of genes in response to diverse stress conditions and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon, bab1_0223-bab1_0226 , is among the most highly activated gene sets in the σ E1 regulon. The proteins encoded by the operon resemble quaternary ammonium-compatible solute importers but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized. Transcription of yehZYXW is activated by the general stress sigma factor σ S in Enterobacteriaceae , which suggests a functional role for this transport system in bacterial stress response across the classes Alphaproteobacteria and Gammaproteobacteria . We present evidence that B. abortus YehZYXW does not function as an importer of known compatible solutes under physiological conditions and does not contribute to the virulence defect of a σ E1 -null strain. The sole in vitro phenotype associated with genetic disruption of this putative transport system is reduced growth in the presence of high Li + ion concentrations. A crystal structure of B. abortus YehZ revealed a class II periplasmic binding protein fold with significant structural homology to Archaeoglobus fulgidus ProX, which binds glycine betaine. However, the structure of the YehZ ligand-binding pocket is incompatible with high-affinity binding to glycine betaine. This is consistent with weak measured binding of YehZ to glycine betaine and related compatible solutes. We conclude that YehZYXW is a conserved, stress-regulated transport system that is phylogenetically and functionally distinct from quaternary ammonium-compatible solute importers. IMPORTANCE Brucella abortus σ E1 regulates transcription in response to stressors encountered in its mammalian host and is necessary for maintenance of chronic infection in a mouse model. The functions of the majority of genes regulated by σ E1 remain undefined. We present a functional/structural analysis of a conserved putative membrane transport system (YehZYXW) whose expression is strongly activated by σ E1 . Though annotated as a quaternary ammonium osmolyte uptake system, experimental physiological studies and measured ligand-binding properties of the periplasmic binding protein (PBP), YehZ, are inconsistent with this function. A crystal structure of B. abortus YehZ provides molecular insight into differences between bona fide quaternary ammonium osmolyte importers and YehZ-related proteins, which form a distinct phylogenetic and functional group of PBPs.
Pathways to Identity. Using Visualization to Aid Law Enforcement in Identification Tasks
The nature of identity has changed dramatically in recent years and has grown in complexity. Identities are defined in multiple domains: biological and psychological elements strongly contribute, but biographical and cyber elements also are necessary to complete the picture. Law enforcement is beginning to adjust to these changes, recognizing identity’s importance in criminal justice. The SuperIdentity project seeks to aid law enforcement officials in their identification tasks through research of techniques for discovering identity traits, generation of statistical models of identity and analysis of identity traits through visualization. We present use cases compiled through user interviews in multiple fields, including law enforcement, and describe the modeling and visualization tools design to aid in those use cases.
Federal Air Pollutant Emission Regulations and Preliminary Estimates of Potential-to-Emit from Biorefineries, Pathway #2: Conversion of Lignocellulosic Biomass to Hydrocarbon Fuels: Fast Pyrolysis and Hydrotreating Bio-oil Pathway
Biorefineries are subject to environmental laws, including complex air quality regulations that aim to protect and improve the quality of the air. These regulations govern the amount of certain types of air pollutants that can be emitted from different types of emission sources. To determine which federal air emission regulations potentially apply to the fast pyrolysis biorefinery, we first identified the types of regulated air pollutants emitted to the ambient environment by the biorefinery or from specific equipment. Once the regulated air pollutants are identified, we review the applicability criteria of each federal air regulation to determine whether the fast pyrolysis biorefinery or specific equipment is subject to it. We then estimate the potential-to-emit of pollutants likely to be emitted from the fast pyrolysis biorefinery to understand the air permitting requirements.
MassIVE MSV000085574 - Pathway discovery and engineering for cleavage of a B-1 lignin-derived biaryl compound: Pathway discovery and engineering for cleavage of a B-1 lignin-derived biaryl compound
Explore the source record for details and available documents.
Pathways to IEC Standards for Heliostat Design Qualification and Site Acceptance in Central Receiver CSP Applications
This paper surveys the existing landscape of standards relevant to heliostats, identifies their gaps, and proposes a path forward to a comprehensive set of heliostat guidelines, technical specifications, and standards under the framework of International Electrotechnical Commission (IEC) TC 117. Gaps in existing guidelines and standards are surveyed using a three-tiered taxonomy: component-level, heliostat-level, and field-level. At each level, the gap analysis is followed by a proposal for a coordinated path forward on the development of standards. At the component level, advances in the understanding of wind loading should inform a technical specification for drives and structures. Reflectors require consolidation of measurement guidelines into existing standards documents. Communications & controls require technical standards to inform their selection and secure implementation. At the heliostat level, IEC 62817 (solar trackers) adequately characterizes drive systems, structures, and electronics, but requires adaptation to heliostats' use patterns, operating modes, and expected life cycles. IEC 62817 does not address heliostat beam quality and pointing accuracy, but the process for determining both is elaborated in the SolarPACES Guideline for Heliostat Performance Testing. This SolarPACES document requires two main modifications: adaptation to IEC language and inclusion of testing after heliostats which have undergone accelerated weathering and mechanical cycling (to understand performance degradation). At the field level, IEC 62862-4-2 addresses the function and control of heliostat fields but does not cover the statistically rigorous testing of heliostat groups, or field performance factors like security and soiling. The addition of documents under IEC-62862-4 is proposed to address this gap.
The mevalonate pathway of isoprenoid biosynthesis supports metabolic flexibility in Mycobacterium marinum
ABSTRACT Isoprenoids are a diverse class of natural products that are essential in all domains of life. Most bacteria synthesize isoprenoids through either the methylerythritol phosphate (MEP) pathway or the mevalonate (MEV) pathway, while a small subset encodes both pathways, including the pathogen Mycobacterium marinum (Mm). It is unclear whether the MEV pathway is functional in Mm, or why Mm encodes seemingly redundant metabolic pathways. Here, we show that the MEP pathway is essential in Mm, while the MEV pathway is dispensable in culture, with the ΔMEV mutant having no growth defect in axenic culture but a competitive growth defect compared to WT Mm. We found that the MEV pathway does not play a role in ex vivo or in vivo acute infection but does play a role in survival of peroxide stress. Metabolite profiling revealed that modulation of the MEV pathway causes compensatory changes in the concentration of MEP intermediates DOXP and CDP-ME, suggesting that the MEV pathway is functional and that the pathways interact at the metabolic level. Finally, the MEV pathway is upregulated early in the shift down to hypoxia, suggesting that it may provide metabolic flexibility to this bacterium. Interestingly, we found that our complemented strains, which vary in copy number of the polyprenyl synthetase idsB2 , responded differently to peroxide and UV stresses, suggesting a role for this gene as a determinant of downstream prenyl phosphate metabolism. Together, these findings suggest that MEV may serve as an anaplerotic pathway to make isoprenoids under stress conditions. IMPORTANCE Organisms from all domains of life utilize isoprenoids to carry out thousands of critical and auxiliary cellular processes, including signaling, maintaining membrane integrity, stress response, and host-pathogen interactions. The common precursor of all isoprenoids is synthesized via one of two biosynthetic pathways. Importantly, some bacteria encode both pathways, including M. marinum . We found that only one pathway is essential in M. marinum , while the nonessential pathway may confer metabolic flexibility to help the bacterium better adapt to various environmental conditions. We also found that the polyprenyl synthetase IdsB2 plays an important role in driving such phenotypes. Further, we demonstrate metabolic interplay between both functional pathways. These insights represent the first characterization of isoprenoid biosynthesis in dual pathway-encoding mycobacteria.
Curation and Computational Design of Bioenergy-Related Metabolic Pathways
Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manually curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate compounds. The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.
Techno-Economic Analysis and Life Cycle Assessment for Guiding Bioenergy Pathway Development
The Center for Bioenergy Innovation (CBI) is a bioenergy research center recently launched by the U.S. Department of Energy Office of Science's Biological and Environmental Research program. CBI's objective is to enable innovations across the bioenergy supply chain through development of poplar and switchgrass phenotypes, microorganisms for consolidated bio-processing (CBP), in which biomass fermentation and conversion is accomplished in a single unit operation, and lignin valorization processes. In addition to basic science, CBI's activities involve the application of techno-economic analysis (TEA) and life cycle assessment (LCA) to the bioenergy pathways under study. TEA and LCA is used to quantify the impacts that research and development breakthroughs have on the economic viability and sustainability of a bioenergy pathway, and to identify drivers for reducing costs and improving sustainability through targeted research efforts. Combining TEA and LCA allows for understanding the economic and sustainability benefits and trade-offs of these integrated bioenergy systems. The focus of this presentation is a parameterized, integrated TEA-LCA model, which will be discussed along with an application to bioenergy pathways currently under study. The model combines data and information developed by CBI researchers into a superstructure of potential bioenergy pathways and their life cycles. Model parameters include feedstock species and phenotype, farming, harvesting, storage and transportation practices, and the microbes used for biomass conversion and lignin valorization, among others. The parameterized TEA-LCA model allows for the rapid quantification of pathway economic and sustainability metrics such as minimum fuel selling price, payback period, fossil fuel consumption and net greenhouse gas emissions. To demonstrate the model, economic and sustainability metrics for a bioenergy pathway utilizing CBP will be quantified and compared to the same metrics for a conventional bioenergy pathway. Results of the comparison will be used to identify and prioritize high-impact research areas within the CBP pathway. fermentation and conversion is accomplished in a single unit operation, and lignin valorization processes. In addition to basic science, CBI's activities involve the application of techno-economic analysis (TEA) and life cycle assessment (LCA) to the bioenergy pathways under study. TEA and LCA is used to quantify the impacts that research and development breakthroughs have on the economic viability and sustainability of a bioenergy pathway, and to identify drivers for reducing costs and improving sustainability through targeted research efforts. Combining TEA and LCA allows for understanding the economic and sustainability benefits and trade-offs of these integrated bioenergy systems. The focus of this presentation is a parameterized, integrated TEA-LCA model, which will be discussed along with an application to bioenergy pathways currently under study. The model combines data and information developed by CBI researchers into a superstructure of potential bioenergy pathways and their life cycles. Model parameters include feedstock species and phenotype, farming, harvesting, storage and transportation practices, and the microbes used for biomass conversion and lignin valorization, among others. The parameterized TEA-LCA model allows for the rapid quantification of pathway economic and sustainability metrics such as minimum fuel selling price, payback period, fossil fuel consumption and net greenhouse gas emissions. To demonstrate the model, economic and sustainability metrics for a bioenergy pathway utilizing CBP will be quantified and compared to the same metrics for a conventional bioenergy pathway. Results of the comparison will be used to identify and prioritize high-impact research areas within the CBP pathway.
Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production
Branched C 5 alcohols are promising biofuels with excellent combustion properties. A mevalonate (MVA)-based isoprenoid biosynthetic pathway for C 5 alcohols was constructed in Escherichia coli using genes from several organisms, and the pathway was optimized to achieve over 50% theoretical yield. Although the MVA pathway is energetically less efficient than the native methylerythritol 4-phosphate (MEP) pathway, implementing the MVA pathway in bacterial hosts such as E. coli is advantageous due to its lack of endogenous regulation. The MVA and MEP pathways intersect at isopentenyl diphosphate (IPP), the direct precursor to isoprenoid-derived C 5 alcohols and initial precursor to longer chain terpenes, which makes independent regulation of the pathways difficult. In pursuit of the complete "decoupling" of the MVA pathway from native cellular regulation, we designed novel IPP-bypass MVA pathways for C 5 alcohol production by utilizing promiscuous activities of two enzymes, phosphomevalonate decarboxylase (PMD) and an E. coli-endogenous phosphatase (AphA). These bypass pathways have reduced energetic requirements, are further decoupled from intrinsic regulation, and are free from IPP-related toxicity. In addition to these benefits, we demonstrate that reduced aeration rate has less impact on the bypass pathway than the original MVA pathway. Finally, we showed that performance of the bypass pathway was primarily determined by the activity of PMD. We designed PMD mutants with improved activity and demonstrated titer increases in the mutant strains. These modified pathways would be a good platform for industrial production of isopentenol and related chemicals such as isoprene.
TEA of a Unique Two-Pathways Process for Post-Combustion CO 2 Capture
A unique two-Pathways process using aqueous sodium glycinate for CO 2 capture from a split flue gas stream emitted from 600 MWe post-combustion coal power plant was developed in Aspen Plus v.10. The split gas flow rate used was 44.75 ton/h and contained 0.0023 mol% SO 2 and 13.33 mol% CO 2 . The process includes a washing unit, a CO 2 absorption unit, a reverse osmosis unit, and a solvent regeneration unit or an ultrafiltration unit. The washing unit uses deionized water to completely remove SO 2 and the CO 2 absorption unit uses SGS to capture at least 90 mol% of the CO 2 in the split flue gas stream. Upon CO 2 and SGS reactions, the resulting liquid products exhibit phase-separation into CO 2 -lean phase and CO 2 -rich phase, allow two distinct pathways. Pathway (i) is to regenerate mostly the CO 2 -rich phase, collect the released CO 2 , and compress it for sequestration purposes. Pathway (ii) is to send the liquid stream from the CO 2 absorption unit to the ultrafiltration unit to separate the solid nanomaterials. The hydraulics and mass transfer characteristics in the washing and CO 2 absorption units were obtained; and techno-economic analysis (TEA) for Pathways (i) and (ii), including Capital Expenditure (CAPEX), Operating Expenditure (OPEX), and Levelized Cost of CO 2 Captured (LCOC), were calculated and compared. The simulation results revealed that the CAPEX, OPEX, and LCOC for Pathway (i) were ($\$12,039,251$), (261 dollar/h), and (54.01 dollar/ton-CO 2 captured), respectively, and those for Pathway (ii) were ($\$5,908,000$), (237.2 dollar/h), and (39.90 dollar/ton-CO 2 captured), respectively. Moreover, in Pathway (ii), 8.19 ton/h of CO 2 were captured to produce 15.62 ton/h NaHCO 3 nanomaterials, which were sold to offset the overall process cost. The LCOC values indicate that Pathway (ii) is more cost-effective than Pathway (i) because LCOC values for Pathway (ii) are much lower than those for Pathway (i).COC values for Pathway (ii) are much lower than those for Pathway (i).
Computationally Guided Discovery and Experimental Validation of Indole-3-acetic Acid Synthesis Pathways
Elucidating the interaction networks associated with secondary metabolite production in microorganisms is an ongoing challenge made all the more daunting by the rate at which DNA sequencing technology reveals new genes and potential pathways. Developing the culturing methods, expression conditions, and genetic systems needed for validating pathways in newly discovered microorganisms is often not possible. Therefore, new tools and techniques are needed for defining complex metabolic pathways. Here, we describe an in vitro computationally assisted pathway description approach that employs bioinformatic searches of genome databases, protein structural modeling, and protein–ligand-docking simulations to predict the gene products most likely to be involved in a particular secondary metabolite production pathway. This information is then used to direct in vitro reconstructions of the pathway and subsequent confirmation of pathway activity using crude enzyme preparations. As a test system, we elucidated the pathway for biosynthesis of indole-3-acetic acid (IAA) in the plant-associated microbe Pantoea sp. YR343. This organism is capable of metabolizing tryptophan into the plant phytohormone IAA. BLAST analyses identified a likely three-step pathway involving an amino transferase, an indole pyruvate decarboxylase, and a dehydrogenase. However, multiple candidate enzymes were identified at each step, resulting in a large number of potential pathway reconstructions (32 different enzyme combinations). Our approach shows the effectiveness of crude extracts to rapidly elucidate enzymes leading to functional pathways. Furthermore, results are compared to affinity purified enzymes for select combinations and found to yield similar relative activities. Further, in vitro testing of the pathway reconstructions revealed the “underground” nature of IAA metabolism in Pantoea sp. YR343 and the various mechanisms used to produce IAA. Importantly, our experiments illustrate the scalable integration of computational tools and cell-free enzymatic reactions to identify and validate metabolic pathways in a broadly applicable manner.
Theoretical study of the decomposition pathways and products of C5- perfluorinated ketone (C5 PFK)
Due to the high global warming potential (GWP) and increasing environmental concerns, efforts on searching the alternative gases to SF{sub 6}, which is predominantly used as insulating and interrupting medium in high-voltage equipment, have become a hot topic in recent decades. Overcoming the drawbacks of the existing candidate gases, C5- perfluorinated ketone (C5 PFK) was reported as a promising gas with remarkable insulation capacity and the low GWP of approximately 1. Experimental measurements of the dielectric strength of this novel gas and its mixtures have been carried out, but the chemical decomposition pathways and products of C5 PFK during breakdown are still unknown, which are the essential factors in evaluating the electric strength of this gas in high-voltage equipment. Therefore, this paper is devoted to exploring all the possible decomposition pathways and species of C5 PFK by density functional theory (DFT). The structural optimizations, vibrational frequency calculations and energy calculations of the species involved in a considered pathway were carried out with DFT-(U)B3LYP/6-311G(d,p) method. Detailed potential energy surface was then investigated thoroughly by the same method. Lastly, six decomposition pathways of C5 PFK decomposition involving fission reactions and the reactions with a transition states were obtained. Important intermediate products were also determined. Among all the pathways studied, the favorable decomposition reactions of C5 PFK were found, involving C-C bond ruptures producing Ia and Ib in pathway I, followed by subsequent C-C bond ruptures and internal F atom transfers in the decomposition of Ia and Ib presented in pathways II + III and IV + V, respectively. Possible routes were pointed out in pathway III and lead to the decomposition of IIa, which is the main intermediate product found in pathway II of Ia decomposition. We also investigated the decomposition of Ib, which can undergo unimolecular reactions to give the formation of IV a, IV b and products of CF{sub 3} + CF-CF{sub 3} in pathway IV. Although IV a is dominant to a lesser extent due to its relative high energy barrier, its complicated decomposition pathway V was also studied and CF{sub 3}, C = CF{sub 2} as well as C-CF{sub 3} species were found as the ultimate products. To complete the decomposition of C5 PFK, pathway V I of Ic decomposition was fully explored and the final products were obtained. Therefore, the integrate decomposition scheme of C5 PFK was proposed, which contains six pathways and forty-eight species (including all the reactants, products and transition states). This work is hopeful to lay a theoretical basis for the insulating properties of C5 PFK.