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 163 records · Page 9

Pathways to excellence: A Federal strategy for science, mathematics, engineering, and technology education

This Strategic Plan was developed by the Federal Coordinating Council for Science, Engineering, and Technology (FCCSET) through its Committee on Education and Human Resources (CEHR), with representatives from 16 Federal agencies. Based on two years of coordinated interagency effort, the Plan confirms the Federal Government's commitment to ensuring the health and well-being of science, mathematics, engineering, and technology education at all levels and in all sectors (i.e., elementary and secondary, undergraduate, graduate, public understanding of science, and technology education). The Plan represents the Federal Government's efforts to develop a five-year planning framework and associated milestones that focus Federal planning and the resources of the participating agencies toward achieving the requisite or expected level of mathematics and science competence by all students. The priority framework outlines the strategic objectives, implementation priorities, and components for the Strategic Plan and serves as a road map for the Plan. The Plan endorses a broad range of ongoing activities, including continued Federal support for graduate education as the backbone of our country's research and development enterprise. The Plan also identifies three tiers of program activities with goals that address issues in science, mathematics, engineering, and technology education meriting special attention. Within each tier, individual agency programs play important and often unique roles that strengthen the aggregate portfolio. The three tiers are presented in descending order of priority: (1) reforming the formal education system; (2) expanding participation and access; and (3) enabling activities.

Source record↗

helixCAM: A platform for programmable cellular assembly in bacteria and human cells

Interactions between cells are indispensable for signaling and creating structure. The ability to direct precise cell-cell interactions would be powerful for engineering tissues, understanding signaling pathways, and directing immune cell targeting. In humans, intercellular interactions are mediated by cell adhesion molecules (CAMs). However, endogenous CAMs are natively expressed by many cells and tend to have cross-reactivity, making them unsuitable for programming specific interactions. Here, we showcase “helixCAM,” a platform for engineering synthetic CAMs by presenting coiled-coil peptides on the cell surface. helixCAMs were able to create specific cell-cell interactions and direct patterned aggregate formation in bacteria and human cells. Based on coiled-coil interaction principles, we built a set of rationally designed helixCAM libraries, which led to the discovery of additional high-performance helixCAM pairs. Finally, we applied this helixCAM toolkit for various multicellular engineering applications, such as spherical layering, adherent cell targeting, and surface patterning.

59 BASIC BIOLOGICAL SCIENCES↗

Elucidation of odd-chain dicarboxylate metabolism in Acinetobacter baylyi and application to polyethylene upcycling

Polyethylene (PE) is a versatile polymer, but its end-of-life management is challenging due to its recalcitrant structure. We present a promising approach combining chemical degradation and bio-upcycling to convert postconsumer PE waste into a value-added bioproduct. Specifically, PE was degraded into acetic acid and C 4 –C 7 dicarboxylic acids by nitric acid. We then elucidated the catabolic pathways for glutarate (C 5 ) and pimelate (C 7 ) in the nonmodel bacterium Acinetobacter baylyi ADP1 through RNA sequencing, phenotyping, and enzymatic assays. Whole-genome sequencing of evolved isolates also identified a crucial IclR family transcriptional regulator, DcaS, which acts as a repressor of dicarboxylate metabolism. The reverse-engineered strain exhibited enhanced substrate utilization compared to the wild-type strain. Using rational metabolic engineering, the PE deconstruction products were bioconverted into the valuable chemical lycopene, highlighting the potential of this microbial chassis to produce value-added bioproducts from postconsumer PE waste, thus promoting a circular economy for plastics.

metabolic engineering↗

Rewiring Aromatic Compound Consumption: Chromosomal Amplification and Evolution of a Foreign Pathway in Acinetobacter baylyi ADP1

Rational engineering strategies that seek to harness the remarkable diversity of microbial metabolism can be limited by incomplete biological knowledge. As described here, a novel approach to address this challenge involved replacing a native pathway for degrading lignin-derived aromatic compounds via ortho cleavage of protocatechuate in Acinetobacter baylyi ADP1 with a foreign meta-cleavage pathway that uses different enzymes, metabolites, and redox carriers. This alteration may improve lignin valorization and coordinate catabolism with bioproduction strategies. When a 14-kbp region of foreign DNA was inserted in the chromosome, the heterologous genes failed to confer growth on target substrates. Regional gene dosage was increased using a synthetic DNA fragment to promote recombination, and higher copy number enabled growth. During adaptive laboratory evolution, compensatory mutations arose that permit growth with one copy of the foreign genes. This complex metabolic remodeling was accomplished without assumptions about the impediments that initially prevented growth. To understand the changes that emerged, a novel transformation assay identified a combination of mutations sufficient for the new phenotype. Three unexpected changes were revealed: loss of one foreign enzyme, loss of one native enzyme, and loss of a two-component transcriptional regulatory system. This study establishes that large multicopy tandem arrays of poorly adapted pathway genes can confer new functions and improve understanding of metabolism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Plant terpene specialized metabolism: complex networks or simple linear pathways?

From the perspectives of pathway evolution, discovery and engineering of plant specialized metabolism, the nature of the biosynthetic routes represents a critical aspect. Classical models depict biosynthesis typically from an end-point angle and as linear, for example, connecting central and specialized metabolism. As the number of functionally elucidated routes increased, the enzymatic foundation of complex plant chemistries became increasingly well understood. The perception of linear pathway models has been severely challenged. With a focus on plant terpenoid specialized metabolism, we review here illustrative examples supporting that plants have evolved complex networks driving chemical diversification. The completion of several diterpene, sesquiterpene and monoterpene routes shows complex formation of scaffolds and their subsequent functionalization. These networks show that branch points, including multiple sub-routes, mean that metabolic grids are the rule rather than the exception. This concept presents significant implications for biotechnological production.

60 APPLIED LIFE SCIENCES↗

From Filamentary Failure to Durable Halide Perovskite Memristors

Halide perovskites have emerged as promising materials for memristive devices. While their pronounced electrochemical reactivity and fast ionic mobility enable numerous advantages including low-voltage operation and fast switching, the same features also render perovskite-based memristors vulnerable to metallic shunts and poor endurance, limiting their practical applications. Here, we elucidate both the resistive switching and failure mechanisms in perovskite memristors with a fluorine-doped tin oxide (FTO)/methylammonium lead triiodide (MAPbI3)/Ag structure and demonstrate a strategy to substantially enhance device durability. As opposed to commonly invoked filamentary mechanisms, electrical, structural, and spectroscopic analyses reveal that resistive switching arises from interfacial barrier modulation by reversible Ag redox reactions that drive electrochemical doping/dedoping within the perovskite. Device failure, however, originates from metallic Ag0 filamentation that ultimately forms permanent conductive pathways. Introducing an ultrathin Al2O3 interlayer at the inert-electrode interface improves device endurance by more than 30-fold, exceeding 15,000 switching cycles, without compromising other performance metrics. Interfacial characterization indicates that the Al2O3 layer modifies wettability of Ag deposits, promoting planar island growth rather than through-film filamentation. These findings establish a clear link between interfacial electrochemistry, metal precipitation behavior, and memristor reliability, highlighting inert-electrode interfacial engineering as an effective pathway toward durable perovskite-based memristors.

14 SOLAR ENERGY↗

Engineering Escherichia coli for selective 1-decanol production using the reverse β-oxidation (rBOX) pathway

1-Decanol has great value in the pharmaceutical and fragrance industries and plays an important role in the chemical industry. Here, in this study, we engineered Escherichia coli to selectively synthesize 1-decanol by using enzymes of the core reverse β-oxidation (rBOX) pathway and termination module with overlapping chain-length specificity. Through screening for acyl-CoA reductase termination enzymes and proper regulation of rBOX pathway expression, a 1-decanol titer of 1.4 g/L was achieved. Further improvements were realized by engineering pyruvate dissimilation to ensure the generation of NADH through pyruvate dehydrogenase (PDH) and reducing byproduct synthesis via a tailored YigI thioesterase knockout, increasing 1-decanol titer to 1.9 g/L. The engineered strain produced about 4.4 g/L 1-decanol with a yield of 0.21 g/g in 36 hours in a bi-phasic fermentation that used a dodecane overlay to increase 1-decanol transport and reduce its toxicity. Adjustment of pathway expression (varying inducer concentration) and cell growth (oxygen availability) enabled 1-decanol production at 6.1 g/L (0.26 g/g yield) and 10.05 g/L (0.2 g/g yield) using rich in shake flasks and bioreactor, respectively. Remarkably, the use of minimal medium resulted in 1-decanol production at 100% specificity at 2.8 g/L (0.14 g/g yield) and a per cell mass yield higher than rich medium. These 1-decanol titers, yields and purity are at least 10-fold higher than others reported to date and the engineered strain shows great potential for industrial production. Taken together, our findings suggest that using rBOX pathway and termination enzymes of proper chain-length specificity in combination with optimal chassis engineering should be an effective approach for the selective production of alcohols.

1-decanol↗

Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in Zymomonas mobilis

Genetically engineered microbes have the potential to increase efficiency in the bioeconomy by overcoming growth-limiting production stress. Screens of gene perturbation libraries against production stressors can identify high-value engineering targets, but follow-up experiments needed to guard against false positives are slow and resource-intensive. In principle, the use of orthogonal gene perturbation approaches could increase recovery of true positives over false positives because the strengths of one technique compensate for the weaknesses of the other, but, in practice, two parallel screens are rarely performed at the genome scale. Here, we screen genome-scale CRISPRi (CRISPR interference) knockdown and transposon insertion libraries of the bioenergy-relevant Alphaproteobacterium, Zymomonas mobilis, against growth inhibitors commonly found in deconstructed plant material. Integrating data from the two gene perturbation techniques, we established an approach for defining engineering targets with high specificity. This allowed us to identify all known genes in the cytochrome bc1 and cytochrome c synthesis pathway as potential targets for engineering resistance to phenolic acids under anaerobic conditions, a subset of which we validated using precise gene deletions. Strikingly, this finding is specific to the cytochrome bc1 and cytochrome c pathway and does not extend to other branches of the electron transport chain. We further show that exposure of Z. mobilis to ferulic acid causes substantial remodeling of the cell envelope proteome, as well as the downregulation of TonB-dependent transporters. Our work provides a generalizable strategy for identifying high-value engineering targets from gene perturbation screens that is broadly applicable.

CRISPRi↗

Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology

Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures.

59 BASIC BIOLOGICAL SCIENCES↗

Triggering the stringent response enhances synthetic methanol utilization in Escherichia coli

Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, i.e. the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here in this paper, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. By activating the stringent/stress response via ppGpp overproduction, or DksA and RpoS overexpression, we demonstrate improved biosynthesis of proteinogenic amino acids via endogenous upregulation of amino acid synthesis pathway genes. Thus, we were able to achieve biosynthesis of several limiting amino acids from methanol-derived carbon, in contrast to the control methylotrophic E. coli strain. This study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via stringent/stress response activation.

60 APPLIED LIFE SCIENCES↗

Introducing furanocoumarin biosynthetic genes in tomato results in coumarins accumulation and impacts growth

Over the past three decades, efforts to decipher plant metabolism have shed light on key enzymes driving specialized metabolite biosynthesis. Although only few pathways have been completely investigated to date, their characterization paves the way for exploring the potential effects of specialized metabolites on plant physiology. Among them is the linear furanocoumarin pathway, which was recently completed to produce up to psoralen. In this study, we report the first metabolic engineering of the linear furanocoumarin pathway to enable artificial psoralen production in tomato, through the integration of four genes coding for the enzymes: Umbelliferone Synthase (PsDiox), Demethylsuberosin Synthase (PsPT1), Marmesin Synthase (FcCYP76F112) and Psoralen Synthase (PsCYP71AJ3). Metabolic analyses confirmed the detection of small quantities of psoralen in the transgenic tomato line, but also highlighted a larger accumulation of coumarins and particularly scopoletin. Using morphophysiological and multi-omics analyses, we explorate how such metabolic modifications, could impact growth and affect plant physiology.

coumarins↗

Enabling room-temperature ferromagnetism in few-layered MoS 2 films via strain engineering

Strain engineering presents a promising pathway for modulating the physical properties of two-dimensional (2D) transition metal dichalcogenides materials. Here, in this study, we investigate the strain-induced magnetic behavior of diamagnetic MoS 2 films prepared by the DC magnetron sputtering technique. By applying +1% tensile strain to few-layered MoS 2 films (∼3.5 nm), we observe the emergence of room-temperature ferromagnetism with a magnetization saturation of about ∼130 emu/cm 3 , in stark contrast to bulk films (∼40 nm), which remain diamagnetic under similar conditions. Raman spectroscopy reveals a pronounced reduction in the intensity and the splitting of the E′ mode in 1% strained few-layered films, indicating a possible bond elongation and symmetry breaking under tensile stress. Additionally, x-ray absorption spectroscopy at the Mo M 3 edge further confirms a strain-induced electronic structure modification in few-layered films, with no corresponding shift observed in bulk counterparts. Moreover, the strain-induced magnetic and structural changes are largely reversible upon strain release. We attribute the origin of ferromagnetism in few-layered films to the combined influence of tensile strain and defect-assisted bond weakening, which facilitates crystal field transitions within the Mo 4d orbitals. These findings demonstrate that strain engineering can effectively induce and modulate magnetism in 2D materials, providing opportunities for developing strain-controlled spintronic applications.

36 MATERIALS SCIENCE↗

MultiSector Dynamics: Advancing the Science of Complex Adaptive Human-Earth Systems

The field of MultiSector Dynamics (MSD) explores the dynamics and co-evolutionary pathways of human and Earth systems with a focus on critical goods, services, and amenities delivered to people through interdependent sectors. This commentary lays out core definitions and concepts, identifies MSD science questions in the context of the current state of knowledge, and describes ongoing activities to expand capacities for open science, leverage revolutions in data and computing, and grow and diversify the MSD workforce. Central to our vision is the ambition of advancing the next generation of complex adaptive human-Earth systems science to better address interconnected risks, increase resilience, and improve sustainability. This will require convergent research and the integration of ideas and methods from multiple disciplines. Understanding the tradeoffs, synergies, and complexities that exist in coupled human-Earth systems is particularly important in the context of energy transitions and increased future shocks.

Reed, Patrick↗

Regulatory interventions improve the biosynthesis of limiting amino acids from methanol carbon to improve synthetic methylotrophy in Escherichia coli

Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methylotrophs have proved successful, autonomous methylotrophy, that is, the ability to utilize methane or methanol as sole carbon and energy substrates, has not yet been realized. Here, we address an important limitation of autonomous methylotrophy in E. coli: the inability of the organism to synthesize several amino acids when grown on methanol. We targeted global and local amino acid regulatory networks. Those include removal of amino acid allosteric feedback inhibition (argA H15Y , ilvA L447F , hisG E271K , leuA G462D , proB D107N , thrA S345F, trpE S40F ), knockouts of transcriptional repressors (ihfA, metJ); and overexpression of amino acid biosynthetic operons (hisGDCBHAFI, leuABCD, thrABC, trpEDCBA) and transcriptional regulators (crp, purR). Compared to the parent methylotrophic E. coli strain that was unable to synthesize these amino acids from methanol carbon, these strategies resulted in improved biosynthesis of limiting proteinogenic amino acids (histidine, leucine, lysine, methionine, phenylalanine, threonine, tyrosine) from methanol carbon. In several cases, improved amino acid biosynthesis from methanol carbon led to improvements in methylotrophic growth in methanol minimal medium supplemented with a small amount of yeast extract. Here, this study addresses a key limitation currently preventing autonomous methylotrophy in E. coli and possibly other synthetic methylotrophs and provides insight as to how this limitation can be alleviated via global and local regulatory modifications.

60 APPLIED LIFE SCIENCES↗

Biochemical parallels between catabolic pathways for lignin-associated aromatic dimers

Lignin is one of the most common biopolymers on Earth. In nature, lignin is primarily deconstructed by fungi into mixtures of aromatic compounds that are then assimilated by bacteria and fungi. Industrially, lignin is primarily generated as a byproduct of pulp and paper production and burned for process heat. However, if the appropriate assimilatory pathways were identified, deconstructed lignin could be funneled into value-added products using engineered bacteria. Foundational work has described pathways for assimilation of diverse monomeric aromatic compounds such as protocatechuate, ferulate, and syringate, as well as select dimers including those with β-O-4 and 5-5 interunit linkages. Recent advances have elucidated additional pathways for dimer assimilation, including pathways for new substrates as well as parallel pathways for previously characterized substrates. Comparing these dimer assimilation pathways can illuminate the underlying biochemical logic of assimilation for lignin-associated aromatic dimers and provide opportunities for metabolic engineering to enhance lignin valorization.

Sphingomonas↗

Bio-based oxalic acid production in Issatchenkia orientalis enables sustainable rare earth recovery

The growing demand for rare earth elements (REEs) in clean energy and high-tech industries underscores the need for sustainable recovery methods and a reliable supply of processing chemicals. Here, we establish a microbial platform using the acid-tolerant yeast Issatchenkia orientalis SD108 to produce bio-oxalic acid for REE recovery. By introducing an oxaloacetate cleavage pathway and applying metabolic engineering, the engineered strain produces 39.53 g·L -1 oxalic acid at pH 4.0 in fed-batch fermentation. The crude fermentation broth, used without purification, efficiently precipitates over 99% neodymium (Nd), 99% dysprosium (Dy), and 98% lanthanum (La) from individual REE chloride solutions. Recovery from a low-grade ore leachate achieves over 99% total recovery. X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) confirm that REE oxalates precipitated with bio-oxalic acid closely resemble those obtained using commercial oxalic acid. Techno-economic analysis (TEA) and life cycle assessment (LCA) further demonstrate that bio-oxalic acid can be produced at a competitive price of $1.79·kg -1 while reducing carbon intensity (CI) by 112% to 63.5% with and without electricity displacement, respectively, relative to the fossil-based benchmark. These results highlight bio-oxalic acid as a green, economically viable alternative to synthetic oxalate for sustainable REE recovery.

59 BASIC BIOLOGICAL SCIENCES↗

Bridging length scales in organic mixed ionic–electronic conductors through internal strain and mesoscale dynamics

Understanding the structural and dynamic properties of disordered systems at the mesoscale is crucial. This is particularly important in organic mixed ionic-electronic conductors (OMIECs), which undergo significant and complex structural changes when operated in an electrolyte. Here, in this study, we investigate the mesoscale strain, reversibility and dynamics of a model OMIEC material under external electrochemical potential using operando X-ray photon correlation spectroscopy. Our results reveal that strain and structural hysteresis depend on the sample's cycling history, establishing a comprehensive kinetic sequence bridging the macroscopic and microscopic behaviours of OMIECs. Furthermore, we uncover the equilibrium and non-equilibrium dynamics of charge carriers and material-doping states, highlighting the unexpected coupling between charge carrier dynamics and mesoscale order. These findings advance our understanding of the structure-dynamics-function relationships in OMIECs, opening pathways for designing and engineering materials with improved performance and functionality in non-equilibrium states during device operation. Understanding mesoscale structure and dynamics in organic mixed ionic-electronic conductors is crucial. Mesoscale strain kinetics and structural hysteresis have been studied, and they uncover the coupling between charge carrier dynamics and mesoscale order in organic mixed ionic-electronic conductors.

36 MATERIALS SCIENCE↗

Quantum guidelines for solid-state spin defects

Defects with associated electron and nuclear spins in solid-state materials have a long history relevant to quantum information science going back to the first spin echo experiments with silicon dopants in the 1950s. Since the turn of the century, the field has rapidly spread to a vast array of defects and host crystals applicable to quantum communication, sensing, and computing. From simple spin resonance to long-distance remote entanglement, the complexity of working with spin defects is fast advancing, and requires an in-depth understanding of their spin, optical, charge, and material properties in this modern context. This is especially critical for discovering new relevant systems dedicated to specific quantum applications. In this review, we therefore expand upon all the key components with an emphasis on the properties of defects and the host material,on engineering opportunities and other pathways for improvement. Finally, this review aims to be as defect and material agnostic as possible, with some emphasis on optical emitters,providing a broad guideline for the field of solid-state spin defects for quantum information.

36 MATERIALS SCIENCE↗