Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “pathway engineering”

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.

At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

With its ability to catabolize a wide variety of carbon sources and a growing engineering toolkit, Pseudomonas putida KT2440 is emerging as an important chassis organism for metabolic engineering. Despite advances in our understanding of the organism, many gaps remain in our knowledge of the genetic basis of its metabolic capabilities. The gaps are particularly noticeable in our understanding of both fatty acid and alcohol catabolism, where many paralogs putatively coding for similar enzymes coexist, making biochemical assignment via sequence homology difficult. To rapidly assign function to the enzymes responsible for these metabolisms, we leveraged random barcode transposon sequencing (RB-Tn-Seq). Global fitness analyses of transposon libraries grown on 13 fatty acids and 10 alcohols produced strong phenotypes for hundreds of genes. Fitness data from mutant pools grown on fatty acids of varying chain lengths indicated specific enzyme substrate preferences and enabled us to hypothesize that DUF1302/DUF1329 family proteins potentially function as esterases. From the data, we also postulate catabolic routes for the two biogasoline molecules isoprenol and isopentanol, which are catabolized via leucine metabolism after initial oxidation and activation with coenzyme A (CoA). Because fatty acids and alcohols may serve as both feedstocks and final products of metabolic-engineering efforts, the fitness data presented here will help guide future genomic modifications toward higher titers, rates, and yields. IMPORTANCE To engineer novel metabolic pathways into P. putida , a comprehensive understanding of the genetic basis of its versatile metabolism is essential. Here, we provide functional evidence for the putative roles of hundreds of genes involved in the fatty acid and alcohol metabolism of the bacterium. These data provide a framework facilitating precise genetic changes to prevent product degradation and to channel the flux of specific pathway intermediates as desired.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cyanobacterial circadian regulation enhances bioproduction under subjective nighttime through rewiring of carbon partitioning dynamics, redox balance orchestration, and cell cycle modulation

Abstract Background The industrial feasibility of photosynthetic bioproduction using cyanobacterial platforms remains challenging due to insufficient yields, particularly due to competition between product formation and cellular carbon demands across different temporal phases of growth. This study investigates how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942, and provides insights that suggest potential strategies for enhanced bioproduction. Results After entrainment to light-dark cycles, PCC 7942 cultures transitioned to constant light revealed distinct temporal patterns in sucrose production, exhibiting three-fold higher productivity during subjective night compared to subjective day despite moderate down-regulation of genes from the photosynthetic apparatus. This enhanced productivity coincided with reduced glycogen accumulation and halted cell division at subjective night time, suggesting temporal separation of competing processes. Transcriptome analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism, with over 300 genes showing differential expression across four time points. The subjective night was characterized by altered expression of cell division-related genes and reduced expression of genes involved in glycogen synthesis, while showing upregulation of glycogen degradation pathways, alternative electron flow components, the pentose phosphate pathway, and oxidative decarboxylation of pyruvate. These molecular changes created favorable conditions for product formation through enhanced availability of major sucrose precursors (glucose-1-phosphate and fructose-6-phosphate) and maintained redox balance through multiple mechanisms. Conclusions Our analysis of circadian regulatory rewiring of carbon metabolism and redox balancing suggests two potential approaches that could be developed for improving cyanobacterial bioproduction: leveraging natural circadian rhythms for optimizing cultivation conditions and timing of pathway induction, and engineering strains that mimic circadian-driven metabolic shifts through controlled carbon flux redistribution and redox rebalancing. While these strategies remain to be tested, they could theoretically improve the efficiency of photosynthetic bioproduction by enabling better temporal separation between cell growth, carbon storage accumulation, and product synthesis phases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Development of an Advanced Hydrogen Energy Storage System using Aerogel in a Cryogenic Flux Capacitor

The Cryogenic Flux Capacitor (CFC) is a cold, dense fluid storage core with integrated design features that afford the designer flexibility and provide new possibilities for the storage and discharge of energy. The stored energy, in this case, is represented by hydrogen physically bonded within the nanoscale pores within the aerogel composite blanket material, and the process of bonding or debonding is governed by the principles of physical adsorption (physisorption) and thermodynamics. The large surface area afforded by the nanoporous aerogel (~1,000 m 2 /g) allows for storage densities close to, or in some cases exceeding, that of normal boiling point liquids. Its performance easily exceeds what can be achieved via ambient temperature and high-pressure gas storage for an equivalent volume. CFC storage is predicted to be easily scalable, constructed from readily available commercial materials, and lends itself to a range of pressure applications. The project team designed and manufactured the CFC, integrating it into a set of temperature-controlled flow loops. The CFC test setup was validated against existing data from previous NASA work. Tests used bottled hydrogen gas for test validation. A cryogenic fluid, nitrogen, flowed through a metered control system. Hydrogen temperature, pressure, and flow rates, as well as the temperature control targets, provided all necessary control targets. The team analyzed the recorded data and updated the Technology Maturation Plan based on the results of the test, making recommendations for a follow-up test, scale-up, and maturation pathway. For the engineering development and maturation of CFC hydrogen storage technology, a Techno-Economic Assessment (TEA) and Commercialization Plan for the integration of this technology with various power generation assets were produced. A companion analytical model was developed, experimentally validated, compared against performance metric, and used to tune the model and scale up the technology.

08 HYDROGEN↗
DOE OSTI2025

FY25 Theory and Simulation Performance Target: Development of an integrated modeling framework for fusion reactor design and assessment (Final Report)

This report documents the FY25 Theory and Simulation Performance Target (TSPT) of developing an integrated modeling framework for fusion reactor design and assessment (FREDA). Over Q1-Q4, new capabilities were developed across both plasma and engineering domains and demonstrated on an example representation of a Compact Advanced Tokamak with a Dual Cooled Lead Lithium blanket. This represents a first-of-a-kind demonstration of coupled core-to-wall-to-engineering for a reactor. Self-consistent CESOL workflows were applied to provide core, pedestal, and SOL prediction; new modules were developed for energetic particle stability (FAR3D) and transport (TGLF-EP) analysis; and boundary plasma modeling (SOLPS-ITER, BOUT++/Hermes-3) was expanded to evaluate wall and divertor heat fluxes and interface with engineering thermal analysis. A parameterized CAD tool, TRACER, was expanded to generate medium-fidelity divertor, blanket, and coil geometries; OpenFOAM and Diablo workflows were applied for first-wall and divertor thermal analyses with helium cooling; and reduced-order models were created for high-mass-flux divertor cooling. Magnet multiphysics capabilities were verified between Elmer, Diablo, and a new MFEM-based solver, and workflows enable stress, thermal, and neutron-fluence analysis of TF coils with neutronics-driven heating. Nuclear and blanket analysis workflows were demonstrated, including tritium breeding, transport, and CFD-informed thermo-mechanical assessment. Preliminary multi-fidelity uncertainty quantification workflows were applied to boundary modeling codes and shown to achieve variance reductions with fewer high-fidelity boundary simulations. Key findings highlight the challenges of resolving the ITEP gap to find suitable balance between wall and divertor loads, neutron heating, and practical limits of PFC cooling. Next step priorities are to develop automated workflows to check boundary code convergence and detachment, implement tighter physics-engineering CAD provenance tracking, and inclusion of plasma-material interface models for SLAG and tungsten cracking behavior. Collectively, these developments establish sophisticated capabilities for predictive, multi-fidelity, whole-device modeling that integrates plasma physics, materials, magnets, and nuclear engineering to guide pathways to viable Fusion Pilot Plant design points.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

A Review of Polymeric Nanoparticle Design, Synthesis, and Biomedical Applications

Polymeric nanoparticles (PNPs) are solid particles that contain macromolecular polymers ranging in size from 1-1000 nm. They have a wide variety of structures that are determined by their identity as either natural biopolymers, synthetic polymers or a combination of both. In the design of PNPs, the polymeric system, size, internal structure, additional molecules, and synthetic pathway can be engineered, allowing for a multitude of properties including differing responses to physiological environments and the incorporation of a drug. The easily accessible fine tuning of PNPs allows for a multitude of applications in medicine. PNPs allow for increased pharmacokinetics, efficacy, safety, and targeting strength when utilized as carriers for drugs. Currently there are a wide range of PNPs approved by the Food and Drug Administration for use in clinical settings and many more being investigated in clinical studies. There is also research that is being conducted for the usage of PNPs in controlled drug delivery systems and as carriers through the blood brain barrier to aid in treating neurological diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Corynebacterium glutamicum as an Efficient Omnivorous Microbial Host for the Bioconversion of Lignocellulosic Biomass

Corynebacterium glutamicum has been successfully employed for the industrial production of amino acids and other bioproducts, partially due to its native ability to utilize a wide range of carbon substrates. We demonstrated C. glutamicum as an efficient microbial host for utilizing diverse carbon substrates present in biomass hydrolysates, such as glucose, arabinose, and xylose, in addition to its natural ability to assimilate lignin-derived aromatics. As a case study to demonstrate its bioproduction capabilities, L-lactate was chosen as the primary fermentation end product along with acetate and succinate. C. glutamicum was found to grow well in different aromatics (benzoic acid, cinnamic acid, vanillic acid, and p-coumaric acid) up to a concentration of 40 mM. Besides, 13 C-fingerprinting confirmed that carbon from aromatics enter the primary metabolism via TCA cycle confirming the presence of β-ketoadipate pathway in C. glutamicum . 13 C-fingerprinting in the presence of both glucose and aromatics also revealed coumarate to be the most preferred aromatic by C. glutamicum contributing 74 and 59% of its carbon for the synthesis of glutamate and aspartate respectively. 13 C-fingerprinting also confirmed the activity of ortho-cleavage pathway, anaplerotic pathway, and cataplerotic pathways. Finally, the engineered C. glutamicum strain grew well in biomass hydrolysate containing pentose and hexose sugars and produced L-lactate at a concentration of 47.9 g/L and a yield of 0.639 g/g from sugars with simultaneous utilization of aromatics. Succinate and acetate co-products were produced at concentrations of 8.9 g/L and 3.2 g/L, respectively. Our findings open the door to valorize all the major carbon components of biomass hydrolysate by using C. glutamicum as a microbial host for biomanufacturing.

13C-fingerprinting↗
DOE OSTI2024

Spatiotemporal metabolic responses to water deficit stress in distinct leaf cell-types of poplar

The impact of water-deficit (WD) stress on plant metabolism has been predominantly studied at the whole tissue level. However, plant tissues are made of several distinct cell types with unique and differentiated functions, which limits whole tissue ‘omics’-based studies to determine only an averaged molecular signature arising from multiple cell types. Advancements in spatial omics technologies provide an opportunity to understand the molecular mechanisms underlying plant responses to WD stress at distinct cell-type levels. Here, we studied the spatiotemporal metabolic responses of two poplar ( Populus tremula× P. alba ) leaf cell types -palisade and vascular cells- to WD stress using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). We identified unique WD stress-mediated metabolic shifts in each leaf cell type when exposed to early and prolonged WD stresses and recovery from stress. During water-limited conditions, flavonoids and phenolic metabolites were exclusively accumulated in leaf palisade cells. However, vascular cells mainly accumulated sugars and fatty acids during stress and recovery conditions, respectively, highlighting the functional divergence of leaf cell types in response to WD stress. By comparing our MALDI-MSI metabolic data with whole leaf tissue gas chromatography-mass spectrometry (GC-MS)-based metabolic profile, we identified only a few metabolites including monosaccharides, hexose phosphates, and palmitic acid that showed a similar accumulation trend at both cell-type and whole leaf tissue levels. Overall, this work highlights the potential of the MSI approach to complement the whole tissue-based metabolomics techniques and provides a novel spatiotemporal understanding of plant metabolic responses to WD stress. This will help engineer specific metabolic pathways at a cellular level in strategic perennial trees like poplars to help withstand future aberrations in environmental conditions and to increase bioenergy sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Research and Development Pathways for Powering the Blue Economy with Marine Renewable Energy

As marine renewable energy technology is adapted or designed for Blue Economy end-uses, challenges unique to operation at sea and in remote coastal areas must be addressed to meet demands distinct from utility grid electricity generation. Foundational research and development with this end goal is conducted to broadly enable the initiative of Powering the Blue Economy. Determination of distinct R\&D topics is informed by pathways including an engineering design customer-driven approach and feedback from the creation and administration of prize competitions in the Blue Economy technology space. Critical research outcomes, such as determining the performance of small wave energy converters and benchmarking the reliability for power systems at sea, are among the goals of ten foundational R\&D projects currently underway.

Cavagnaro, Robert J.↗
DOE OSTI2021

Research and Development Pathways for Powering the Blue Economy with Marine Renewable Energy

As marine renewable energy technology is adapted or designed for Blue Economy end-uses, challenges unique to operation at sea and in remote coastal areas must be addressed to meet demands distinct from utility grid electricity generation. Foundational research and development with this end goal is conducted to broadly enable the initiative of Powering the Blue Economy. Determination of distinct R&D topics is informed by pathways including an engineering design customer-driven approach and feedback from the creation and administration of prize competitions in the Blue Economy technology space. Critical research outcomes, such as determining the performance of small wave energy converters and benchmarking the reliability for power systems at sea, are among the goals of ten foundational R&D projects currently underway.

customer discovery↗
DOE OSTI2022

BETO 2021 Peer Review - 1.3.2.001 - Algae Biomass Composition

Addressing critical improvements in biomass productivity and associated biochemical composition is a priority for the economic and sustainable commercial development of biofuels and bioproducts from algae. Capitalizing on pathways that integrate engineering approaches with fundamental biochemistry of photosynthetic organisms will lead to a better understanding of the complex nexus of algae growth rates, productivity and composition. This project focuses on identifying the critical factors for economic development of fuel and bioproduct technologies. Algal compositional characteristics form the foundation of robust economic and business models. This project supports that foundation by developing and validating accurate compositional methods and disseminating them to the greater community. Simultaneously, we build a deep understanding of the dynamic biochemical composition and carbon allocation for biomass value and conversion yields. A co-product portfolio developed under this project demonstrated a 30% increase in intrinsic value. Additionally, an integrated pipeline of molecular diversity mapping for product discovery with quantitative demonstration across species was deployed over the BETO algae program. The advances made here are highly relevant to BETO's multi-year program targets of reducing costs and integrating dynamic biomass composition with conversion processes to provide options for bioproducts, all leveraging the molecular diversity of algae.

algal compositional characteristics↗
DOE OSTI2020

Biosystems Design to Accelerate C 3 -to-CAM Progression

Global demand for food and bioenergy production has increased rapidly, while the area of arable land has been declining for decades due to damage caused by erosion, pollution, sea level rise, urban development, soil salinization, and water scarcity driven by global climate change. In order to overcome this conflict, there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency (WUE). Crassulacean acid metabolism (CAM) species have substantially higher WUE than species performing C 3 or C 4 photosynthesis. CAM plants are derived from C 3 photosynthesis ancestors. However, it is extremely unlikely that the C 3 or C 4 crop plants would evolve rapidly into CAM photosynthesis without human intervention. Currently, there is growing interest in improving WUE through transferring CAM into C 3 crops. However, engineering a major metabolic plant pathway, like CAM, is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C 3 and CAM photosynthesis, as well as overcoming physiometabolic limitations such as diurnal stomatal regulation. Recent advances in CAM evolutionary genomics research, genome editing, and synthetic biology have increased the likelihood of successful acceleration of C 3 -to-CAM progression. Here, we first summarize the systems biology-level understanding of the molecular processes in the CAM pathway. Then, we review the principles of CAM engineering in an evolutionary context. Lastly, we discuss the technical approaches to accelerate the C 3 -to-CAM transition in plants using synthetic biology toolboxes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Metabolic engineering reveals the relative importance of different sugar catabolic pathways during consumption of plant biomass by Aspergillus niger

To evaluate the impact of individual sugar catabolic pathways on the physiology of A. niger when using plant biomass as a carbon source, key pathways converting plant biomass derived monomers were blocked. The resulting deletion mutants were analyzed using wheat bran and sugar beet pulp as substrates. On both substrates, the strongest affected single-pathway mutants were the pentose catabolic pathway (PCP) (Δ xkiA ) and glycolysis (Δ hxkA Δ glkA ) deficient mutants. On wheat bran, which is rich in pentose sugars, blocking the PCP by deletion of xkiA strongly impacted both growth and gene expression. However, the effect was even stronger in Δ hxkA Δ glkA and similar to a strain in which all pathways were blocked, highlighting the crucial role of glycolysis and/or carbon catabolite repression in A. niger physiology. These results demonstrate the complexity of A. niger metabolism during growth on plant biomass and provide insights into aspects to consider during metabolic engineering to obtain fungal cell factories.

aspergillus niger↗
DOE OSTI2020

Engineering Solid Electrolyte Interphase Composition by Assessing Decomposition Pathways of Fluorinated Organic Solvents in Lithium Metal Batteries

Studies have shown fluorinated electrolyte solvents can form desirable solid electrolyte interphase (SEI) in lithium metal batteries. In this study, we develop a detailed mechanistic understanding of two high performing electrolytes, Fluoroethylene Carbonate (FEC) and Difluoroethylene Carbonate (DFEC) to demonstrate minimal structural variations can lead to different decomposition products, and thereby the nature of the SEI. Using density functional theory (DFT) calculations, we find different initial bond-breaking mechanisms between FEC and DFEC. We develop free energy diagrams for the decomposition pathways including both electrochemical and chemical steps. Using the computational Li electrode, we identify the largest limiting potential of 1.77 V for FEC decomposition, associated with the formation of lithium fluoride, lithium oxide and FEC oligomers, and 1.53 V for DFEC, which correspond to the formation of polymerized vinylene carbonate and lithium fluoride. We suggest the formation of oligomers in the case of FEC instead of long polymers may lead to better SEI compactness. We also demonstrate the SEI components of FEC and DFEC are not stable on typical cathode voltage (3.87 V). This study presents a unified electrocatalytic perspective on SEI formation and decomposition.

25 ENERGY STORAGE↗
DOE OSTI2020

Engineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy source

Abstract Caldicellulosiruptor bescii is the most thermophilic cellulolytic organism yet identified (Topt 78 °C). It grows on untreated plant biomass and has an established genetic system thereby making it a promising microbial platform for lignocellulose conversion to bio-products. Here, we investigated the ability of engineered C. bescii to generate alcohols from carboxylic acids. Expression of aldehyde ferredoxin oxidoreductase (aor from Pyrococcus furiosus) and alcohol dehydrogenase (adhA from Thermoanaerobacter sp. X514) enabled C. bescii to generate ethanol from crystalline cellulose and from biomass by reducing the acetate produced by fermentation. Deletion of lactate dehydrogenase in a strain expressing the AOR–Adh pathway increased ethanol production. Engineered strains also converted exogenously supplied organic acids (isobutyrate and n-caproate) to the corresponding alcohol (isobutanol and hexanol) using both crystalline cellulose and switchgrass as sources of reductant for alcohol production. This is the first instance of an acid to alcohol conversion pathway in a cellulolytic microbe.

Biotechnology & Applied Microbiology↗
DOE OSTI2024

ETOP 503689: Pre-optimized cell free lysates for rapid prototyping of genes and pathways

This ETOP project aimed to re-conceive how we engineer complex biological systems by linking pathway design, prospecting, and validation into an integrated framework. Specifically, our vision seeks to advance and interweave high-throughput cell-based systems and rapid cell-free technologies in a way suitable for automation and microdroplet manipulation in a DOE JGI user facility setting. The key technology to be investigated toward this vision is a cell-free platform for combinatorial assembly of pathways by mixing-and-matching crude cell lysates derived from a suite of flux-enhanced background strains, each enriched with pathway enzymes. Through this work, we have established rewired E. coli and S. cerevisiae cells suitable to generated rewired lysates. We have demonstrated that lysates derived from rewired cells can generate higher fluxes of products and can enable a more robust discovery method going from gene to function annotations. Finally, we demonstrate that these rewired lysates can be stored for up to a year and still retain function. Collectively, these technologies enable a more rapid screening approach for enzyme and pathway variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An efficient cre‐based workflow for genomic integration and expression of large biosynthetic pathways in Eubacterium limosum

Abstract Acetogenic Clostridia are obligate anaerobes that have emerged as promising microbes for the renewable production of biochemicals owing to their ability to efficiently metabolize sustainable single‐carbon feedstocks. Additionally, Clostridia are increasingly recognized for their biosynthetic potential, with recent discoveries of diverse secondary metabolites ranging from antibiotics to pigments to modulators of the human gut microbiota. Lack of efficient methods for genomic integration and expression of large heterologous DNA constructs remains a major challenge in studying biosynthesis in Clostridia and using them for metabolic engineering applications. To overcome this problem, we harnessed chassis‐independent recombinase‐assisted genome engineering (CRAGE) to develop a workflow for facile integration of large gene clusters (>10 kb) into the human gut acetogen Eubacterium limosum . We then integrated a non‐ribosomal peptide synthetase gene cluster from the gut anaerobe Clostridium leptum , which previously produced no detectable product in traditional heterologous hosts. Chromosomal expression in E. limosum without further optimization led to production of phevalin at 2.4 mg/L. These results further expand the molecular toolkit for a highly tractable member of the Clostridia, paving the way for sophisticated pathway engineering efforts, and highlighting the potential of E. limosum as a Clostridial chassis for exploration of anaerobic natural product biosynthesis.

Sanford, Patrick A.↗