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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Understanding and eliminating the detrimental effect of thiamine deficiency on the oleaginous yeast Yarrowia lipolytica

Thiamine is a vitamin that functions as a cofactor for key enzymes in carbon and energy metabolism for all living cells. While most plants, fungi and bacteria can synthesize thiamine de novo , the oleaginous yeast, Yarrowia lipolytica , cannot. In this paper, we used proteomics together with physiological characterization to understand key metabolic processes influenced and regulated by thiamine availability and identified the genetic basis of thiamine auxotrophy in Y. lipolytica . Specifically, we found thiamine depletion results in decreased protein abundance of the lipid biosynthesis pathways and energy metabolism (i.e., ATP synthase), attributing to the negligible growth and poor sugar assimilation observed in our study. Using comparative genomics, we identified the missing 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase (THI13) in the de novo thiamine biosynthesis of Y. lipolytica , and discovered an exceptional promoter, P3, that exhibits strong activation or tight repression by low and high thiamine concentrations, respectively. Capitalizing on the strength of our thiamine-regulated promoter (P3) to express the missing gene from Saccharomyces cerevisiae (scTHI13), we engineered the thiamine-prototrophic Y. lipolytica . By comparing this engineered strain to the wildtype, we unveiled the tight relationship linking thiamine availability to lipid biosynthesis and demonstrated enhanced lipid production with thiamine supplementation in the engineered thiamine-prototrophic Y. lipolytica .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

BACKGROUND:Rhodosporidium toruloides is a promising host for the production of bioproducts from lignocellulosic biomass. A key prerequisite for efficient pathway engineering is the availability of robust genetic tools and resources. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering in R. toruloides. RESULTS:This data describes a set of native R. toruloides promoters, characterized over time in four different media commonly used for cultivation of this yeast. The promoter sequences were selected using transcriptional analysis and several of them were found to drive expression bidirectionally. Promoter expression strength was determined by measurement of EGFP and mRuby2 reporters by flow cytometry. A total of 20 constitutive promoters (12 monodirectional and 8 bidirectional) were found, and are expected to be of potential value for genetic engineering of R. toruloides. CONCLUSIONS:A set of robust and constitutive promoters to facilitate genetic engineering of R. toruloides is presented here, ranging from a promoter previously used for this purpose (P7, glyceraldehyde 3-phosphate dehydrogenase, GAPDH) to stronger monodirectional (e.g., P15, mitochondrial adenine nucleotide translocator, ANT) and bidirectional (e.g., P9 and P9R, histones H3 and H4, respectively) promoters. We also identified promoters that may be useful for specific applications such as late-stage expression (e.g., P3, voltage-dependent anion channel protein 2, VDAC2). This set of characterized promoters significantly expands the range of engineering tools available for this yeast and can be applied in future metabolic engineering studies.

09 BIOMASS FUELS↗
DOE OSTI2022

Evaluation of engineered low-lignin poplar for conversion into advanced bioproducts

Lignocellulosic resources are promising feedstocks for the manufacture of bio-based products and bioenergy. However, the inherent recalcitrance of biomass to conversion into simple sugars currently hinders the deployment of advanced bioproducts at large scale. Lignin is a primary contributor to biomass recalcitrance as it protects cell wall polysaccharides from degradation and can inhibit hydrolytic enzymes via non-productive adsorption. Several engineering strategies have been designed to reduce lignin or modify its monomeric composition. For example, expression of bacterial 3-dehydroshikimate dehydratase (QsuB) in poplar trees resulted in a reduction in lignin due to redirection of metabolic flux toward 3,4-dihydroxybenzoate at the expense of lignin. This reduction was accompanied with remarkable changes in the pools of aromatic compounds that accumulate in the biomass. The impact of these modifications on downstream biomass deconstruction and conversion into advanced bioproducts was evaluated in the current study. Using ionic liquid pretreatment followed by enzymatic saccharification, biomass from engineered trees released more glucose and xylose compared to wild-type control trees under optimum conditions. Fermentation of the resulting hydrolysates using Rhodosporidium toruloides strains engineered to produce α-bisabolene, epi-isozizaene, and fatty alcohols showed no negative impact on cell growth and yielded higher titers of bioproducts (as much as + 58%) in the case of QsuB transgenics trees. Our data show that low-recalcitrant poplar biomass obtained with the QsuB technology has the potential to improve the production of advanced bioproducts.

09 BIOMASS FUELS↗
DOE OSTI2023

Enhancing isoprenol production by systematically tuning metabolic pathways using CRISPR interference in E. coli

Regulation of metabolic gene expression is crucial for maximizing bioproduction titers. Recent engineering tools including CRISPR/Cas9, CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa) have enabled effective knock-out, knock-down, and overexpression of endogenous pathway genes, respectively, for advanced strain engineering. CRISPRi in particular has emerged as a powerful tool for gene repression through the use of a deactivated Cas9 (dCas9) protein and target guide RNA (gRNA). By constructing gRNA arrays, CRISPRi has the capacity for multiplexed gene downregulation across multiple orthogonal pathways for enhanced bioproduction titers. In this study, we harnessed CRISPRi to downregulate 32 essential and non-essential genes in E. coli strains heterologously expressing either the original mevalonate pathway or isopentenyl diphosphate (IPP) bypass pathway for isoprenol biosynthesis. Isoprenol remains a candidate bioproduct both as a drop-in blend additive and as a precursor for the high-performance sustainable aviation fuel, 1,4-dimethylcyclooctane (DMCO). Of the 32 gRNAs targeting genes associated with isoprenol biosynthesis, a subset was found to vastly improve product titers. Construction of a multiplexed gRNA library based on single guide RNA (sgRNA) performance enabled simultaneous gene repression, yielding a 3 to 4.5-fold increase in isoprenol titer (1.82 ± 0.19 g/L) on M9-MOPS minimal medium. We then scaled the best performing CRISPRi strain to 2-L fed-batch cultivation and demonstrated translatable titer improvements, ultimately obtaining 12.4 ± 1.3 g/L isoprenol. Our strategy further establishes CRISPRi as a powerful tool for tuning metabolic flux in production hosts and that titer improvements are readily scalable with potential for applications in industrial bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Continuously controlled optical band gap in oxide semiconductor thin films

The optical band gap of the prototypical semiconducting oxide SnO 2 is shown to be continuously controlled through single axis lattice expansion of nanometric films induced by low-energy helium implantation. While traditional epitaxy-induced strain results in Poisson driven multidirectional lattice changes shown to only allow discrete increases in bandgap, we find that a downward shift in the band gap can be linearly dictated as a function of out-of-plane lattice expansion. Our experimental observations closely match density functional theory that demonstrates that uniaxial strain provides a fundamentally different effect on the band structure than traditional epitaxy-induced multiaxes strain effects. In conclusion, charge density calculations further support these findings and provide evidence that uniaxial strain can be used to drive orbital hybridization inaccessible with traditional strain engineering techniques.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2015

Electronic Raman scattering as an ultra-sensitive probe of strain effects in semiconductors

Semiconductor strain engineering has become a critical feature of high-performance electronics because of the significant device performance enhancements that it enables. These improvements, which emerge from strain-induced modifications to the electronic band structure, necessitate new ultra-sensitive tools to probe the strain in semiconductors. Here, we demonstrate that minute amounts of strain in thin semiconductor epilayers can be measured using electronic Raman scattering. We also applied this strain measurement technique to two different semiconductor alloy systems using coherently strained epitaxial thin films specifically designed to produce lattice-mismatch strains as small as 10 -4 . Thus, comparing our strain sensitivity and signal strength in Al x Ga 1-x As with those obtained using the industry-standard technique of phonon Raman scattering, we found that there was a sensitivity improvement of 200-fold and a signal enhancement of 4 × 10 3 , thus obviating key constraints in semiconductor strain metrology.

14 SOLAR ENERGY↗
DOE OSTI2021

Nanoscale decoupling of electronic nematicity and structural anisotropy in FeSe thin films

In a material prone to a nematic instability, anisotropic strain in principle provides a preferred symmetry-breaking direction for the electronic nematic state to follow. This is consistent with experimental observations, where electronic nematicity and structural anisotropy typically appear hand-in-hand. In this work, we discover that electronic nematicity can be locally decoupled from the underlying structural anisotropy in strain-engineered iron-selenide (FeSe) thin films. We use heteroepitaxial molecular beam epitaxy to grow FeSe with a nanoscale network of modulations that give rise to spatially varying strain. We map local anisotropic strain by analyzing scanning tunneling microscopy topographs, and visualize electronic nematic domains from concomitant spectroscopic maps. While the domains form so that the energy of nemato-elastic coupling is minimized, we observe distinct regions where electronic nematic ordering fails to flip direction, even though the underlying structural anisotropy is locally reversed. The findings point towards a nanometer-scale stiffness of the nematic order parameter.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Local strain-dependent electronic structure and perpendicular magnetic anisotropy of a MnGaN 2D magnetic monolayer

Local strain-dependent spin-polarized electronic structure of a two-dimensional (2D) magnetic layer is an exciting property for practical applications. For example, it holds the promise for advanced ultrathin spintronic nanodevices with customized electronic and magnetic properties by local strain engineering. Here, we demonstrate that the spin-polarized electronic structure of a 2D manganese gallium nitride (MnGaN-2D) magnetic monolayer is sensitive to intrinsic local lattice strain, as proven by first-principles calculations and indicated by scanning tunneling spectroscopy measurements. Atomic resolution images reveal a highly non-Gaussian lattice spacing/strain distribution, while the spectroscopy reveals variations in the electronic density of states. Simulations of the MnGaN-2D monolayer based on first-principles calculations, including both isotropic and anisotropic strains, confirm a highly strain-dependent manganese partial density of states. Spin-orbit coupling is included which indicates either out-of-plane perpendicular magnetic anisotropy (PMA) or in-plane magnetic anisotropy, dependent on the type of strain whether compressive or tensile, suggesting that MnGaN-2D is magnetoelastic. The MnGaN-2D PMA is further supported by superconducting quantum interference device magnetometry measurements which reveal a high spin polarization of ~ 79 % at room temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp . PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis ( Spirulina ). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Constructing Polymorphic Nanodomains in BaTiO 3 Films via Epitaxial Symmetry Engineering

Ferroelectric materials owning a polymorphic nanodomain structure usually exhibit colossal susceptibilities to external mechanical, electrical, and thermal stimuli, thus holding huge potential for relevant applications. Despite the success of traditional strategies by means of complex composition design, alternative simple methods such as strain engineering have been intensively sought to achieve a polymorphic nanodomain state in lead-free, simple-composition ferroelectric oxides in recent years. Here, a nanodomain configuration with morphed structural phases is realized in an epitaxial BaTiO3 film grown on a (111)-oriented SrTiO3 substrate. Using a combination of experimental and theoretical approaches, it is revealed that a threefold rotational symmetry element enforced by the epitaxial constraint along the [111] direction of BaTiO3 introduces considerable instability among intrinsic tetragonal, orthorhombic, and rhombohedral phases. Such phase degeneracy induces ultrafine ferroelectric nanodomains (1-10 nm) with low-angle domain walls, which exhibit significantly enhanced dielectric and piezoelectric responses compared to the (001)-oriented BaTiO3 film with uniaxial ferroelectricity. Therefore, the finding highlights the important role of epitaxial symmetry in domain engineering of oxide ferroelectrics and facilitates the development of dielectric capacitors and piezoelectric devices.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Metabolic model guided strain design of cyanobacteria

Cyanobacteria are oxygenic photoautotrophs that serve as potential platforms for the production of biochemicals from cheap and renewable raw materials – sunlight, water, and carbon dioxide. Systems level analysis of the metabolic network of these organisms could enable the successful engineering of these organisms for the enhanced production of target chemicals. Metabolic modeling techniques including both stoichiometric and kinetic modeling with a genome-wide coverage enable a global assessment of metabolic capabilities. Recent studies guided by such modeling techniques have engineered strains for the enhanced production of valuable chemicals such as ethanol, n-butanol, 1,3-propanediol, glycerol, limonene, and isoprene from CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quantum Photon Sources in WSe 2 Monolayers Induced by Weakly Localized Strain Fields

Quantum emitters in semiconductor transition metal dichalcogenide (TMD) monolayers hold great promise for many quantum optics applications due to the intriguing properties afforded by the host materials. The creation of localized excitonic states in two-dimensional semiconductors is also fundamentally interesting. Local strain engineering of TMD monolayers has been attested to be a viable approach for creating quantum emitters. However, despite the ubiquitous existence of local topography variations in the structures used to create strain gradients in the TMD monolayers, an understanding of their influence on the strain fields and exciton trapping is notably lacking, especially on the nanoscale. In this study, we investigate WSe 2 monolayers deposited on the edges of asfabricated trenches, which are deemed to induce 1D delocalized strain profiles in the monolayers, and observe optical signatures of weakly confined excitonic states supporting biexciton emission. Here, our numerical simulations of the strain distributions suggest that the quantum emitters originate from quasi-1D like localized strain profiles induced by local topography variations at the trench edges. These findings have strong implications toward the controlled creation of quantum emitters in TMD monolayers and their efficient coupling to photonic structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Manipulating Interlayer Excitons for Near-Infrared Quantum Light Generation

Interlayer excitons (IXs) formed at the interface of van der Waals materials possess various novel properties. In parallel development, strain engineering has emerged as an effective means for creating 2D quantum emitters. Here, exploring the intersection of these two exciting areas, we use MoS2/WSe2 heterostructure as a model system and demonstrate how strain, defects, and layering can be utilized to create defect-bound IXs capable of bright, robust, and tunable quantum light emission in the technologically important near-infrared spectral range. Our work presents defect-bound IXs as a promising platform for pushing the performance of 2D quantum emitters beyond their current limitations.

2D heterostructures↗
DOE OSTI2026

Multi-modal characterization of nitrate reduction nano-catalysts with periodic strain distribution

Strain engineering serves as a pivotal strategy to optimize catalytic activity in electrocatalysis. However, the catalyst sizes under industrial conditions are usually large and even beyond nanometer regime. The critical methodological limitations on strain imaging of such catalysts with both large field of view and high spatial resolution obscure the mechanistic understanding of strain-performance correlations. Here, we present an optimized four-dimensional scanning transmission electron microscopy (4D-STEM) method to acquire strain mapping of both bulk and surface across particles up to 500 nm with 0.6 nm spatial resolution and 0.55% precision. We observe the ripple-like periodic strain coupled with elemental fluctuations inside a perovskite-type hydroxide CuCoSn(OH) 6 and find it correlated to electrocatalytic nitrate reduction (NO 3 – RR) absorption energy to achieve the 92.6% Faradaic efficiency and long-term test over 1000 h at membrane electrode assembly (MEA) for ammonia electrosynthesis. This universal framework design offers a practical method that not only develops an advanced measurement combining multi-modal characterization techniques but also reveals the intrinsic structure-property constitutive law of industry-level catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Twinned nanostructure of VO 2 thin films grown on r-cut sapphire

Due to strong electron-phonon interactions, strain engineering is a powerful tool to control quantum critical phenomena in strongly correlated oxides. Exploring this possibility requires understanding the nanoscale structure of quantum materials and the role it plays in forming the strain landscape. In this work, we used a combination of x-ray nanoimaging and reciprocal space mapping to study the nanostructure of the archetypal Mott insulator VO 2 featuring an insulator-to-metal and structural phase transitions. We found that VO 2 thin films grown on r-cut sapphire consist of two intertwined crystal lattices, permanently inclined with respect to each other. This persistent pattern of twin domains stands out from the symmetry breaking induced by the structural phase transition and conceivably originates from the post-growth strain relaxation process. We propose a model explaining the formation of twin domains and the emergence of anisotropy in the film nanostructure. Our work suggests using miscut substrates to suppress either one or the other twin that can serve as a new tool to control strain in VO 2 films.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Theory of strain phase equilibria and diagrams

Chemical phase equilibria and phase diagrams are well established and have served as indispensable guides for designing materials through chemical tuning. However, a general thermodynamic theory for strain phase equilibria remains elusive despite extensive studies which have revealed dramatic impacts of mechanical strain on the stability of phases and domain states in solid-state materials. Here, we establish the thermodynamic theory of strain equilibria and a general framework for efficiently constructing multidomain and multiphase diagrams of arbitrarily strained solids under incoherent conditions. As examples, we obtain temperature-strain phase diagrams of ferroelectric PbTiO 3 , strongly correlated VO 2 , and unconventional ferroelectric Hf 0.5 Zr 0.5 O 2 . We reveal the analogs of the Gibbs phase rules, multiple- and multi-critical points, common-tangent construction, and level rule in strain equilibria to those in the familiar chemical phase equilibria. Finally, our strain equilibria theory offers a powerful framework for predicting the thermodynamic stability of structural phases and domains in strained solids and for guiding the strain engineering of their functional properties.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Membrane-Inlet Mass Spectrometry Enables a Quantitative Understanding of Inorganic Carbon Uptake Flux and Carbon Concentrating Mechanisms in Metabolically Engineered Cyanobacteria

Photosynthesis uses solar energy to drive inorganic carbon (Ci) uptake, fixation, and biomass formation. In cyanobacteria, Ci uptake is assisted by carbon concentrating mechanisms (CCM), and CO 2 fixation is catalyzed by RubisCO in the Calvin-Benson-Bassham (CBB) cycle. Understanding the regulation that governs CCM and CBB cycle activities in natural and engineered strains requires methods and parameters that quantify these activities. Here, we used membrane-inlet mass spectrometry (MIMS) to simultaneously quantify Ci concentrating and fixation processes in the cyanobacterium Synechocystis 6803 . By comparing cultures acclimated to ambient air conditions to cultures transitioning to high Ci conditions, we show that acclimation to high Ci involves a concurrent decline of Ci uptake and fixation parameters. By varying light input, we show that both CCM and CBB reactions become energy limited under low light conditions. A strain over-expressing the gene for the CBB cycle enzyme fructose-bisphosphate aldolase showed higher CCM and carbon fixation capabilities, suggesting a regulatory link between CBB metabolites and CCM capacity. While the engineering of an ethanol production pathway had no effect on CCM or carbon fixation parameters, additional fructose-bisphosphate aldolase gene over-expression enhanced both activities while simultaneously increasing ethanol productivity. These observations show that MIMS can be a useful tool to study the extracellular Ci flux and how CBB metabolites regulate Ci uptake and fixation.

09 BIOMASS FUELS↗
DOE OSTI2020

Stretchable electrochemical energy storage devices

The increasingly intimate contact between electronics and the human body necessitates the development of stretchable energy storage devices that can conform and adapt to the skin. Therefore, the development of stretchable batteries and supercapacitors has received significant attention in recent years. This review provides an overview of the general operating principles of batteries and supercapacitors and the requirements to make these devices stretchable. The following sections provide an in-depth analysis of different strategies to convert the conventionally rigid electrochemical energy storage materials into stretchable form factors. Namely, the strategies of strain engineering, rigid island geometry, fiber-like geometry, and intrinsic stretchability are discussed. A wide range of materials are covered for each strategy, including polymers, metals, and ceramics. By comparing the achieved electrochemical performance and strain capability of these different materials strategies, we allow for a side-by-side comparison of the most promising strategies for enabling stretchable electrochemical energy storage. The final section consists of an outlook for future developments and challenges for stretchable supercapacitors and batteries.

25 ENERGY STORAGE↗